BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716520.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,196,222 number of mapped reads = 1,079,525 (90.24%) number of supplementary alignments = 4,182 (0.35%) number of secondary alignments = 0 number of mapped bases = 62,631,317 bp number of sequenced bases = 62,612,467 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,285 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3464 >>>>>>> ACTG content number of A's = 16,116,895 bp (25.74%) number of C's = 11,702,511 bp (18.69%) number of T's = 20,164,627 bp (32.21%) number of G's = 14,626,706 bp (23.36%) number of N's = 1,728 bp (0%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 318,243 number of insertions = 4,441 mapped reads with insertion percentage = 0.41% number of deletions = 11,915 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.35% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.204X There is a 1.84% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5034858 0.02019998176855094 0.3487282840005605 chr2 243199373 5285174 0.02173185701428597 0.26038489308405893 chr3 198022430 4173854 0.021077682967530497 0.156384922003033 chr4 191154276 4055657 0.021216668990444137 0.16804133064066712 chr5 180915260 3773889 0.02085998162896817 0.15680919979522298 chr6 171115067 3635826 0.02124784254094936 0.17478496216675532 chr7 159138663 3465153 0.021774425740902447 0.23594779642563504 chr8 146364022 3183936 0.021753542684144058 0.1967436586474469 chr9 141213431 2623207 0.018576186283583748 0.17255426488451758 chr10 135534747 2980074 0.02198752767067179 0.20673835824161801 chr11 135006516 2844212 0.02106722019254241 0.18242554028187757 chr12 133851895 2829275 0.02113735483535739 0.15811403002230318 chr13 115169878 1953776 0.016964296862413974 0.1396102689058833 chr14 107349540 1871416 0.017432920532309687 0.14503892998963333 chr15 102531392 1799153 0.017547338087441553 0.1427967139762505 chr16 90354753 1816327 0.020102174370395322 0.15918935765938974 chr17 81195210 1673228 0.02060747179544212 0.1596751668755817 chr18 78077248 1668070 0.021364354440361423 0.2799541633452468 chr19 59128983 1283361 0.021704432156392745 0.2501180499386594 chr20 63025520 1363547 0.021634839347616647 0.16225164254666444 chr21 48129895 823572 0.017111443937286794 0.15116470987153918 chr22 51304566 748481 0.014588974400446151 0.12980290862230895 chrMT 16571 5191 0.31325810150262506 0.6188424991163447 chrX 155270560 3544080 0.022825189784850392 0.17607834011666929 chrY 59373566 196000 0.0033011323591377348 0.09632386193107523