BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716103.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 = 1,299,508 number of mapped reads = 1,053,327 (81.06%) number of supplementary alignments = 3,362 (0.26%) number of secondary alignments = 0 number of mapped bases = 58,340,300 bp number of sequenced bases = 58,323,817 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,022 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.0823 >>>>>>> ACTG content number of A's = 13,407,978 bp (22.99%) number of C's = 12,451,497 bp (21.35%) number of T's = 17,159,347 bp (29.42%) number of G's = 15,303,436 bp (26.24%) number of N's = 1,559 bp (0%) GC percentage = 47.59% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 309,376 number of insertions = 5,126 mapped reads with insertion percentage = 0.48% number of deletions = 9,705 mapped reads with deletion percentage = 0.91% homopolymer indels = 33.39% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 0.1712X There is a 1.71% of reference with a coverageData >= 1X There is a 0.12% 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 5970009 0.023951831999648256 0.20390192885895567 chr2 243199373 4805419 0.019759175119254933 0.20810016863444292 chr3 198022430 3713720 0.01875403710579655 0.15412464974664894 chr4 191154276 3700497 0.019358693289183864 0.17273634644928124 chr5 180915260 3388554 0.01873006179799316 0.14912825917658942 chr6 171115067 3058200 0.017872184218587835 0.14927896158392667 chr7 159138663 3411730 0.021438724793107003 0.18897651487618952 chr8 146364022 3421714 0.023378108590101466 0.17510031792577493 chr9 141213431 2650262 0.018767775708246903 0.16130765247061993 chr10 135534747 3105038 0.022909534777823433 0.24224921390867435 chr11 135006516 2329648 0.017255818970989517 0.17129476764910043 chr12 133851895 2738616 0.020460046531279964 0.15609647660478293 chr13 115169878 1146552 0.009955311405296444 0.10817492719721739 chr14 107349540 1897410 0.017675064094359417 0.14731816091314634 chr15 102531392 1128150 0.011002971655744223 0.1154707787454457 chr16 90354753 1546943 0.017120770614026247 0.15410074953977657 chr17 81195210 2260695 0.027842713874377565 0.1928212535841542 chr18 78077248 1559143 0.01996923610832185 0.18616257763229688 chr19 59128983 1569754 0.02654796210514901 0.21060960603275664 chr20 63025520 1543290 0.024486747590499847 0.17711383904920733 chr21 48129895 762653 0.01584572332850508 0.15087478427281692 chr22 51304566 637897 0.012433532719095607 0.12533641532535297 chrMT 16571 3851 0.23239394122261783 0.5251533756639644 chrX 155270560 1810201 0.011658365887261565 0.12545930734699023 chrY 59373566 180354 0.0030376144158159543 0.10606054964766327