Spelling Inconsistencies in the Quran
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In the most widespread version of the Arabic Quran (qira'a Hafs in the Uthmani script) there are inconsistencies and apparent errors in the spelling of many words. It would not be possible to include all the errors in a wiki article, as there are a large number of these errors and numerous other errors in other "qira'at" or readings of the Qur'an. More grammatical errors can be found in a book الأخطاء اللغوية في القرآن ("Linguistic errors in the Koran") by Sami Aldeeb (in Arabic). The errors listed here, it should be noted, are not differences between different qira'aat, but rather are spelling inconsistencies within the Hafs qira'a. Some of these differences occur in the Uthmani script, which is older than the more modern imla'i script. Furthermore, the differences are in the spelling, and not in the pronunciation (recitation). In some cases Islamic scholars have added diacritics and super scripted notations to indicate the missing letters and sounds that are to be pronounced.
In the name of (باسم)
The word "name" in Arabic is اسم (ism). If one adds the preposition "in" (ب, bi), it's باسم (bism, or with the genitive ending bismi). However at basmalas ("In the name of...") at the beginning of suras and in 27:30 and 11:41 it's written as بسم without the alif:
In the name of (بسم) Allah, the Entirely Merciful, the Especially Merciful.
In several other such cases, however, the alif is included (56:74, 56:96, 69:52, 96:1). For example in the first verse (in historical order):
Recite in the name of (باسم) your Lord who created -
The name Abraham (إبراهيم, ibraaheem) occurs 69 times in the Quran.  In the Uthmani script the letter ا (alif) in the middle is missing, so it's written as إبرهيم. in the second sura, the letter ي is also missing, so it's written as إبرهم. All suras except the 2nd have إبرهيم, but all 15 occurrences in sura al-baqara (in 2:124, 1:125 ..2:260) have إبرهم with the letter ي missing, suggesting, perhaps, that it was transcribed by a different scribe.
Son of mother (ابن أم)
In the verse 20:94, the two words are joined together:
[Aaron] said, "O son of my mother (يبنؤم, ya-bna-umma), do not seize [me] by my beard or by my head. Indeed, I feared that you would say, 'You caused division among the Children of Israel, and you did not observe [or await] my word.' "
In 7:150 it was written separately and without the vocative particle ya:
And when Moses returned to his people, angry and grieved, he said, "How wretched is that by which you have replaced me after [my departure]. Were you impatient over the matter of your Lord?" And he threw down the tablets and seized his brother by [the hair of] his head, pulling him toward him. [Aaron] said, "O son of my mother (ابن أم, ibna umma), indeed the people oppressed me and were about to kill me, so let not the enemies rejoice over me and do not place me among the wrongdoing people."
Show you (أريكم)
In 7:145 it's written with the letter و as أوريكم.
And We wrote for him on the tablets [something] of all things - instruction and explanation for all things, [saying], "Take them with determination and order your people to take the best of it. I will show you (سأوريكم, sa-uureekum) the home of the defiantly disobedient."
sa- (س) prefix marks the future tense. The same form is in 21:37:
Man was created of haste. I will show you (سأوريكم) My signs, so do not impatiently urge Me.
In 40:29, it was written without the letter و:
O my people, sovereignty is yours today, [your being] dominant in the land. But who would protect us from the punishment of Allah if it came to us?" Pharaoh said, "I do not show you (أريكم) except what I see, and I do not guide you except to the way of right conduct."
About what (عما)
The words عن (about, of) and ما (what, which) are written many times together as عما. For example:
..And Allah is not unaware of what (عما) you do.
..And if they do not desist from what (عما) they are saying, there will surely afflict the disbelievers among them a painful punishment.
In one verse (7:166) it is written separately, although the ن is still not pronounced in recitation:
So when they were insolent about that which (عن ما) they had been forbidden, We said to them, "Be apes, despised."
With diacritics, the "absorbed" ن is indicated by a shadda on مّ.
Promise, appointment (ميعاد)
It was written with an alif after ع in 3:9, 3:194, 13:31, 34:30 and 39:20.
Our Lord, surely You will gather the people for a Day about which there is no doubt. Indeed, Allah does not fail in His promise (ميعاد)
In 8:42, the alif after ع is missing:
[Remember] when you were on the near side of the valley, and they were on the farther side, and the caravan was lower [in position] than you. If you had made an appointment [to meet], you would have missed the appointment (الميعد). But [it was] so that Allah might accomplish a matter already destined - that those who perished [through disbelief] would perish upon evidence and those who lived [in faith] would live upon evidence; and indeed, Allah is Hearing and Knowing.
The messenger (الرسول)
Here the difference is in the accusative definite form. It's written as الرسولَ (with a fatha above ل). For example:
..And We did not make the qiblah which you used to face except that We might make evident who would follow the Messenger (الرسولَ) from who would turn back on his heels..
However in the verse 33:66 an alif is added at the end:
The Day their faces will be turned about in the Fire, they will say, "How we wish we had obeyed Allah and obeyed the Messenger (الرسولا)."
The final alif would be added to the accusative form if the word was indefinite (رسول would become رسولا). However, in the verse the word is in the definite form الرسول.
The same problem is in the verse 33:67 with the word السبيلا.
It was written as طغى in 20:24, 20:43, 20:45, 53:17, 53:52, 79:17, 79:37, 96:6.
Go to Pharaoh. Indeed, he has transgressed (طغى)
But in one verse 69:11 it was written as طغا:
Indeed, when the water overflowed (طغا), We carried your ancestors in the sailing ship
It's not a different word. In imla'i script it's written as طغى in 69:11 as well.
In verse 51:52 it was written with an alif:
Similarly, there came not to those before them any messenger except that they said, "A magician (ساحر, saahir) or a madman."
But in verse 40:24 without an alif:
To Pharaoh, Haman and Qarun; but they said, "[He is] a magician (سحر) and a liar."
A similar thing happened to the word احسان - it was written 11 times without the alif after س as احسن, but one time with it as احسان.
Also the word آيات appeared 50 times without the alif and 2 times with it.
The grammatical context is exactly the same (والذين سعوا في آياتنا معجزين) but in the second case an alif is missing:
But the ones who strove (سعوا) against Our verses, [seeking] to cause failure - those are the companions of Hellfire.
But those who strive (سعو) against Our verses [seeking] to cause failure - for them will be a painful punishment of foul nature.
The difference is only in translation, the words are both "3rd person masculine plural perfect verb"  and in the imla'i script they are both written as سعوا.
A similar thing happened to the word يعفوا, it appeared 4 times with the alif and one time without it.
A tree (شجرة)
It appears more than a dozen times (20:120, 37:62, 37:146...) in the common form شجرة (with ة), however in the verse 44:43 it's written with ت:
Indeed, the tree (شجرت, shajarat) of zaqqum
A similar thing happened to other words ending on ة like نعمة, لعنة, كلمة, سنة, رحمة.
Wretched is what (بئسما)
It was written 3 times as بئسما in 2:90, 2:93 and 7:150.
How wretched is that for which (بئسما, bi'samaa) they sold themselves - that they would disbelieve in what Allah has revealed through [their] outrage that Allah would send down His favor upon whom He wills from among His servants. So they returned having [earned] wrath upon wrath. And for the disbelievers is a humiliating punishment.
6 times (2:102, 3:187, 5:62, 5:63, 5:79, 5:80) separately as بئس ما:
And wretched is that which (فبئس ما, fa-bi'sa maa) they purchased.
There are more examples where similar things happened with words like إنما and أينما.
The word is written almost 200 times as سموت (without the two alifs). For example:
Do you not consider how Allah has created seven heavens (سموت) in layers
In one verse it's written with one alif:
And He completed them as seven heavens (سموات) within two days and inspired in each heaven its command..
A similar thing happened to the word حسنات. It was written 36 times with the alif and 3 times without it (as حسنت).
The guided one (المهتدي)
The word muhtadee is written as المهتدى in 7:178.
Whoever Allah guides - he is the [rightly] guided (المهتدى); and whoever He sends astray - it is those who are the losers.
In 17:97 it is written as المهتدِ:
And whoever Allah guides - he is the [rightly] guided (المهتدِ); and whoever He sends astray - you will never find for them protectors besides Him..
The word was 11 times written as شركاء. For example:
Or do they have partners (شركاء)? Then let them bring their partners, if they should be truthful.
Two times it was written as شركاؤا in 6:94 and 42:21.
Or have they other deities (شركؤا) who have ordained for them a religion to which Allah has not consented? But if not for the decisive word, it would have been concluded between them. And indeed, the wrongdoers will have a painful punishment.
A similar thing happened with the word بلاء becoming بلؤا and أنباء becoming أنبؤا and ملأ becoming ملؤا.
This word, which was translated as "humbled", "humiliated" or "contemptible", appears two times in the Quran. One time an alif is present (after د), other time it's omitted:
And your Lord says, "Call upon Me; I will respond to you." Indeed, those who disdain My worship will enter Hell [rendered] contemptible (داخرين, daakhireen).
And [warn of] the Day the Horn will be blown, and whoever is in the heavens and whoever is on the earth will be terrified except whom Allah wills. And all will come to Him humbled (دخرين, daakhireen).
With diacritics, the missing alif is indicated by a small "dagger alif" above.
A lamp (سراج)
Allah made an [illuminating / burning] lamp (سراج, siraaj) in the sky:
And one who invites to Allah, by His permission, and an illuminating lamp (وسراجا).
And made the moon therein a [reflected] light and made the sun a burning lamp (سراجا)?
And made [therein] a burning lamp (سراجا)
However in this verse he made it without an alif after ر:
Blessed is He who has placed in the sky great stars and placed therein a [burning] lamp (سرجا) and luminous moon.
(The alif after ج marks the accusative case)
In the second sura, it was writen two times with an alif:
And We shaded you with clouds (الغمام) and sent down to you manna and quails, [saying], "Eat from the good things with which We have provided you." And they wronged Us not - but they were [only] wronging themselves.
Do they await but that Allah should come to them in covers of clouds (الغمام) and the angels [as well] and the matter is [then] decided? And to Allah [all] matters are returned.
In two other verses the alif is missing:
..Every people knew its watering place. And We shaded them with clouds (الغمم) and sent down upon them manna and quails, [saying], "Eat from the good things with which We have provided you."..
And [mention] the Day when the heaven will split open with [emerging] clouds (بالغمم), and the angels will be sent down in successive descent.
A similar thing happened to the word تراب. It was written 14 times with the alif, but 3 times without it (ترب).
In the verse 12:25 was written as لدى:
And they both raced to the door, and she tore his shirt from the back, and they found her husband at (لدى) the door. She said, "What is the recompense of one who intended evil for your wife but that he be imprisoned or a painful punishment?"
In the verse 40:18 as لدا:
And warn them, [O Muhammad], of the Approaching Day, when hearts are at (لدا) the throats, filled [with distress]. For the wrongdoers there will be no devoted friend and no intercessor [who is] obeyed.
This name is mentioned 3 times in the 20th sura.
[ Allah ] said, "But indeed, We have tried your people after you [departed], and the Samiri (السامرى) has led them astray."
They said, "We did not break our promise to you by our will, but we were made to carry burdens from the ornaments of the people [of Pharaoh], so we threw them [into the fire], and thus did the Samiri (السامرى) throw."
When it's written for the third time, the alif after س is missing (ي in the beginning is for the vocative):
[Moses] said, "And what is your case, O Samiri (يسمرى)?"
Their marks (سيماهم)
It was written without an alif (as سيمهم) in 2:273, 7:46, 7:48, 47:30, 55:41.
The criminals will be known by their marks (بسيمهم, bi-seemaahum), and they will be seized by the forelocks and the feet.
In 48:29 alif appeared:
Muhammad is the Messenger of Allah ; and those with him are forceful against the disbelievers, merciful among themselves. You see them bowing and prostrating [in prayer], seeking bounty from Allah and [His] pleasure. Their mark (سيماهم, seemaahum) is on their faces from the trace of prostration. That is their description in the Torah..
Riba, usury, interest (ربا)
It was written 7 times with the letter و as ربوا. The و is not pronounced, it's just there. For example:
O you who have believed, do not consume usury (الرِوبا, ar-ribaa), doubled and multiplied, but fear Allah that you may be successful.
In 30:39 it was written without the و as ربا:
And whatever you give for interest (ربا) to increase within the wealth of people will not increase with Allah . But what you give in zakah, desiring the countenance of Allah - those are the multipliers.
Something similar happened to the words صلاة and حياة. Most of the times they were written as صلوة and حيوة and only a few times with an alif.
The word شيء (shay) is written without an alif. The "a" is indicated only by a fatha above the letter َش:
Indeed, Our word to a thing (لشىء, li-shay'in) when We intend it is but that We say to it, "Be," and it is.
English "to" is indicated by Arabic ل (li-). The word was written cca 200 times without an alif. However in the verse 18:23 the word is written with an alif:
And never say of anything [literally "to something"] (لشاىء, li-shay'in), "Indeed, I will do that tomorrow,"
It is written as وراء in more than a dozen verses. For example:
..And when you ask [his wives] for something, ask them from behind (من وراء) a partition..
In the verse 42:51 it was written as ورائ:
And it is not for any human being that Allah should speak to him except by revelation or from behind (من ورائ) a partition ..
Wood, thicket (الأيكة)
It was written two times as الأيكة (al-ayka):
And the companions of the thicket (الأيكة) were [also] wrongdoers.
And the companions of the the thicket (الأيكة) and the people of Tubba'. All denied the messengers, so My threat was justly fulfilled.
Two times as لئيكة (also pronounced as al-ayka):
And [the tribe of] Thamud and the people of Lot and the companions of the thicket (لئيكة). Those are the companies.
The companions of the thicket (لئيكة) denied the messengers
O [vocative] (أيها)
It was written 150 times as أيها. For example:
[Abraham] said, "Then what is your business [here], O (أيها) messengers?"
Three times as أيه. For example:
.. And turn to Allah in repentance, all of you, O (أيه) believers, that you might succeed.
The word Quran (قرءان in Uthmani script) was mentioned 70 times . 68 times alif after ء was present. For example (the second alif after ن only marks the accusative case):
[It is] an Arabic Qur'an (قرءانا), without any deviance that they might become righteous.
In 2 cases (12:2, 43:3) the alif after ء is missing:
Indeed, We have sent it down as an Arabic Qur'an (قرءنا) that you might understand.
- quran.com - Quran in Uthmani script (not in corpus.quran.com)
- al-quran.info - Quran in imla'i script
- http://corpus.quran.com/qurandictionary.jsp?q=%3CiboraAhiym (the Quran quotes here use the imla'i script, but if you go to http://quran.com/2/124 you'll see Uthmani إبرهم)
- http://corpus.quran.com/wordmorphology.jsp?location=(34:5:2), http://corpus.quran.com/wordmorphology.jsp?location=(22:51:2)