BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716856.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 = 649,310 number of mapped reads = 583,850 (89.92%) number of supplementary alignments = 2,668 (0.41%) number of secondary alignments = 0 number of mapped bases = 33,520,480 bp number of sequenced bases = 33,512,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,404 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8641 >>>>>>> ACTG content number of A's = 8,095,321 bp (24.16%) number of C's = 6,401,483 bp (19.1%) number of T's = 10,633,511 bp (31.73%) number of G's = 8,381,292 bp (25.01%) number of N's = 414 bp (0%) GC percentage = 44.11% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 168,187 number of insertions = 1,899 mapped reads with insertion percentage = 0.32% number of deletions = 5,422 mapped reads with deletion percentage = 0.92% homopolymer indels = 41.54% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.1278X There is a 1.03% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 4083967 0.01638498224644343 0.19713075596639418 chr2 243199373 2966713 0.012198686877371185 0.15629692847703172 chr3 198022430 2341913 0.011826503694556218 0.11325926295094856 chr4 191154276 1563514 0.008179330500563848 0.09663258315827093 chr5 180915260 1571523 0.008686514338259801 0.09760463097102891 chr6 171115067 2700095 0.015779411172483136 0.15037694198069892 chr7 159138663 1402017 0.008810033800522756 0.11869017177438548 chr8 146364022 2406619 0.016442695186389453 0.13860142922601018 chr9 141213431 1443885 0.010224841856579492 0.12073625751797258 chr10 135534747 1565431 0.011550034471971973 0.13393731811899195 chr11 135006516 1161410 0.00860262181715733 0.10911100486466072 chr12 133851895 1519137 0.011349387320963966 0.11227964754707505 chr13 115169878 795388 0.00690621552972384 0.08606016077367039 chr14 107349540 724400 0.006748049409433892 0.0920610660027846 chr15 102531392 1015803 0.009907238945902539 0.10489676998330458 chr16 90354753 908897 0.010059205186472039 0.10802647424107602 chr17 81195210 679515 0.00836890501299276 0.0971666529972344 chr18 78077248 670985 0.008593860787716288 0.16367154700724254 chr19 59128983 715125 0.012094322677594506 0.15694416429516778 chr20 63025520 596185 0.009459422151534808 0.1013332738686706 chr21 48129895 321421 0.006678198653871985 0.08805957179893723 chr22 51304566 540459 0.010534325541317316 0.10695786624195713 chrMT 16571 27990 1.6890954076398528 1.5520381776997185 chrX 155270560 1722253 0.011091948145224698 0.11702536104018176 chrY 59373566 75835 0.0012772519002816844 0.04206296663526042