BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524518.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 = 2,376,651 number of mapped reads = 2,185,689 (91.97%) number of supplementary alignments = 9,881 (0.42%) number of secondary alignments = 0 number of mapped bases = 127,756,888 bp number of sequenced bases = 127,716,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,850 duplication rate = 5.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.967 >>>>>>> ACTG content number of A's = 30,529,903 bp (23.9%) number of C's = 23,080,545 bp (18.07%) number of T's = 41,893,312 bp (32.8%) number of G's = 32,211,001 bp (25.22%) number of N's = 1,802 bp (0%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 653,500 number of insertions = 8,440 mapped reads with insertion percentage = 0.38% number of deletions = 23,753 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.16% >>>>>>> Coverage mean coverageData = 0.0413X std coverageData = 0.3821X There is a 3.42% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12406325 0.049774499859721516 0.7644504774420622 chr2 243199373 10146484 0.041720847693139405 0.46597702428553456 chr3 198022430 6896075 0.03482471657377399 0.21901821629551427 chr4 191154276 7228361 0.037814278347610704 0.28022217155197154 chr5 180915260 6905571 0.038170196367072626 0.2294776115497312 chr6 171115067 5390113 0.031499932147997234 0.27221779342229285 chr7 159138663 6420308 0.04034411172601092 0.4326112539686389 chr8 146364022 11688782 0.07986103306179984 0.3981047017462714 chr9 141213431 5404926 0.03827487202686832 0.293721860091245 chr10 135534747 6742740 0.049749161371880526 0.42692377575935103 chr11 135006516 4392839 0.03253797764842698 0.3130220260646027 chr12 133851895 5884686 0.0439641590430976 0.2463894196188901 chr13 115169878 2846834 0.024718563998131524 0.1848805572569075 chr14 107349540 3015454 0.028090050502312353 0.2008902392210663 chr15 102531392 3351564 0.03268817417401297 0.21423569814308543 chr16 90354753 4086769 0.045230260327312276 0.2700013589376984 chr17 81195210 4493132 0.05533740229257366 0.29233254034252265 chr18 78077248 2989659 0.038291039663693065 0.5609047839652932 chr19 59128983 2687892 0.045458113155776754 0.5155929386989966 chr20 63025520 3698873 0.058688496342433984 0.29081130761052254 chr21 48129895 1792330 0.03723943299689309 0.2740336525712752 chr22 51304566 1083567 0.021120283913911287 0.1732528257233873 chrMT 16571 78023 4.708406251885824 3.3860592975210277 chrX 155270560 7653141 0.0492890667747962 0.2894943901108328 chrY 59373566 472440 0.007957076386484855 0.2685397711805851