BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525170.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 = 1,510,025 number of mapped reads = 1,357,252 (89.88%) number of supplementary alignments = 5,653 (0.37%) number of secondary alignments = 0 number of mapped bases = 78,972,519 bp number of sequenced bases = 78,951,407 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,668 duplication rate = 1.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7108 >>>>>>> ACTG content number of A's = 20,571,157 bp (26.06%) number of C's = 14,571,485 bp (18.46%) number of T's = 25,299,802 bp (32.04%) number of G's = 18,506,476 bp (23.44%) number of N's = 2,487 bp (0%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 379,205 number of insertions = 4,908 mapped reads with insertion percentage = 0.36% number of deletions = 12,695 mapped reads with deletion percentage = 0.93% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2409X There is a 2.33% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6269858 0.025154834017444633 0.4321063644441349 chr2 243199373 6757134 0.027784339723606114 0.25073961904346265 chr3 198022430 5335703 0.026944942550194945 0.17553399796264443 chr4 191154276 5264327 0.027539676904742637 0.19493274682490266 chr5 180915260 4834935 0.02672486002562747 0.1762512386420456 chr6 171115067 4583027 0.026783304827271582 0.18706466286223347 chr7 159138663 4263324 0.02678999508749172 0.2654591810714675 chr8 146364022 4046794 0.02764883025693295 0.2812118530425393 chr9 141213431 3311206 0.023448237016491725 0.22856077799844388 chr10 135534747 3746660 0.027643538523741074 0.2326217875726835 chr11 135006516 3625416 0.026853637197777922 0.22961709744144318 chr12 133851895 3588363 0.026808458707289873 0.1787112792467319 chr13 115169878 2525880 0.021931776293103306 0.15725299370358695 chr14 107349540 2401523 0.02237105999708988 0.17609292283696107 chr15 102531392 2244136 0.02188730647487942 0.15810309493887365 chr16 90354753 2205426 0.02440852226113661 0.1774493944243693 chr17 81195210 2017487 0.024847364764497806 0.17662934376662184 chr18 78077248 2150015 0.0275370233336093 0.39832855921135824 chr19 59128983 1452470 0.024564433993393732 0.3108046346228824 chr20 63025520 1630916 0.02587707328713829 0.17599803848528117 chr21 48129895 1053493 0.021888537259430962 0.1781162409979011 chr22 51304566 863456 0.01683000300597027 0.13851383366463085 chrMT 16571 6964 0.420252247902963 0.7213798116356972 chrX 155270560 4562420 0.029383677111746102 0.20457318810282737 chrY 59373566 231586 0.0039004899924656704 0.10970805082352192