BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525172.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 = 2,229,288 number of mapped reads = 2,049,835 (91.95%) number of supplementary alignments = 6,686 (0.3%) number of secondary alignments = 0 number of mapped bases = 120,240,685 bp number of sequenced bases = 120,203,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,449 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8925 >>>>>>> ACTG content number of A's = 30,962,612 bp (25.76%) number of C's = 22,362,124 bp (18.6%) number of T's = 38,460,883 bp (32%) number of G's = 28,415,175 bp (23.64%) number of N's = 2,815 bp (0%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 603,094 number of insertions = 8,625 mapped reads with insertion percentage = 0.42% number of deletions = 23,303 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.18% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3548X There is a 3.44% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 12648260 0.05074514939724062 0.6316407698978214 chr2 243199373 9958664 0.04094855951787343 0.46522464577474404 chr3 198022430 9177491 0.04634571447285037 0.2416317900256404 chr4 191154276 6622127 0.03464284000636219 0.21851978245157014 chr5 180915260 5286090 0.029218596595997487 0.1892639244989864 chr6 171115067 7482149 0.043725833915022806 0.2585050538748811 chr7 159138663 8883161 0.05582025657712105 0.6550330395322617 chr8 146364022 6896073 0.047115902567913856 0.31894884747953506 chr9 141213431 4036469 0.028584171997067333 0.26651432612400067 chr10 135534747 6369313 0.046993949086723864 0.3902973250455399 chr11 135006516 5411483 0.040083124580446175 0.27312347880947846 chr12 133851895 5346640 0.039944447555262476 0.22311410381742353 chr13 115169878 3609437 0.0313401130806095 0.19705990826774994 chr14 107349540 4406786 0.04105081400441958 0.22820580391741224 chr15 102531392 3201621 0.031225763520308005 0.1997380265991539 chr16 90354753 3678040 0.040706657678539614 0.2498106274659303 chr17 81195210 2216963 0.027304110673523722 0.19023470684680166 chr18 78077248 2600011 0.033300494914984706 0.48444063947908605 chr19 59128983 2088857 0.0353271254470925 0.45410237905436246 chr20 63025520 2545181 0.04038333995498966 0.22558673772626417 chr21 48129895 1537444 0.031943639187245264 0.2083864454548071 chr22 51304566 974751 0.018999303102963584 0.15126423801644268 chrMT 16571 41613 2.511194255023837 2.1851812432296502 chrX 155270560 4897729 0.031543191445950865 0.21662930319692228 chrY 59373566 324332 0.005462565613795203 0.1337640606729549