The phrase “Bismillah ir-Rahman ir-Rahim” (Arabic: بسم الله الرحمن الرحيم), abbreviated as Bismillah, is recited at the beginning of each sura of the Quran except for the 9th sura (Sura at-Tawbah).
Though each sura of the Quran, except sura 9, traditionally starts with a Bismillah, there are different opinion among Islamic scholars on whether these Bismillahs should be considered as part of the Quran text, and if so, whether they should receive individual aya numbers, i.e., be numbered as aya 1 in the containing suras.
Different views on this issue has led to different numbering systems for the Quran over the past centuries. In the most common numbering system currently in use, Bismillah is numbered as the first aya in the first sura (Sura al-Fatihah), but receives no number in the subsequent suras.
Medina Mushaf follows the currently most common numbering system, namely, it gives number 1 to the Bismillah of Sura 1, and leaves Bismillas in other suras without number. While Bismillahs are not individually numbered in suras 2 to 114, they are considered as part of the Quran text in Medina Mushaf. A strong indication for this fact is that Bismillahs at the beginning of two suras, i.e. suras 95 and 97, are written slightly differently, with a Shadda above Bah. The reason for adding these Shaddas is that the preceding suras end with a Majzoom letter Beh, causing the two Behs (one from the word at the end of sura, and the other from Bismillah) to be merged by the Arabic Idgham rule:
Note that the letter Beh at the end of the above two suras have no diacritic in Medina Mushaf because of being merged to the succeeding Beh of Bismillah.
Tanzil Quran text closely follows the same standards set by Medina Mushaf. In particular, it considers Bismillahs as part of the Quran text. Each aya in Tanzil Quran text is encoded in one line, leading to a text file with exactly 6236 lines. To avoid adding extra lines and/or using non-standard numbering systems (like giving number 0 to Bismillahs), Bismillahs of suras 2 to 114 are encoded in the same line together with the first aya of those suras. This enables us to have Bismillahs in the Quran text file, while keeping the number of lines in the file matching the number of ayas in the Quran. This is in particular useful for those applications who have been using old (Bismillah-less) Quran text files, to easily adopt themselves with Tanzil Quran text.
Note: Application that are using Tanzil Quran text are recommended to add a newline after each Bismillah on the fly (not in the Quran text file) to display Bismillahs in separate lines, just like in the Medina Mushaf.