BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525162.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 = 2,324,110 number of mapped reads = 2,145,545 (92.32%) number of supplementary alignments = 7,243 (0.31%) number of secondary alignments = 0 number of mapped bases = 125,274,293 bp number of sequenced bases = 125,235,149 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,650 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8628 >>>>>>> ACTG content number of A's = 30,732,405 bp (24.54%) number of C's = 24,456,954 bp (19.53%) number of T's = 39,170,748 bp (31.28%) number of G's = 30,872,158 bp (24.65%) number of N's = 2,884 bp (0%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 628,984 number of insertions = 8,129 mapped reads with insertion percentage = 0.38% number of deletions = 24,503 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 0.3421X There is a 3.57% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% 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 13235176 0.05309987171506385 0.5682447655545972 chr2 243199373 10479356 0.043089568327135445 0.4937280967094184 chr3 198022430 9843940 0.04971123725731474 0.2504827895242896 chr4 191154276 7026902 0.03676037045595569 0.2258993656352391 chr5 180915260 5697082 0.03149033420398036 0.19798642998894914 chr6 171115067 6432157 0.03758965889310028 0.25209505551881217 chr7 159138663 7433367 0.04671000032217187 0.5317843913590414 chr8 146364022 6278283 0.04289498822326705 0.3127304422073824 chr9 141213431 4568130 0.0323491184064496 0.2617280088731607 chr10 135534747 6837323 0.05044701193856953 0.3721895870407296 chr11 135006516 5929657 0.043921265252115683 0.29660940326103274 chr12 133851895 5760383 0.0430354983020599 0.23424602282904847 chr13 115169878 3782202 0.032840201497825676 0.20466128496283728 chr14 107349540 4839214 0.04507903806574299 0.2448436385772932 chr15 102531392 3528183 0.034410758804484 0.20777054426808508 chr16 90354753 3505679 0.038799054655154666 0.24725572510927546 chr17 81195210 2812332 0.034636673764376 0.21918590721892417 chr18 78077248 2692732 0.03448804957879663 0.5049733547781857 chr19 59128983 2437832 0.041229053440678995 0.425720880014354 chr20 63025520 2493744 0.0395672102348382 0.2250514980330539 chr21 48129895 1629807 0.03386267516270293 0.22037421413897726 chr22 51304566 1091342 0.02127182987962514 0.16034501206055862 chrMT 16571 126345 7.624464425804115 4.781903981377134 chrX 155270560 6454308 0.04156813757868845 0.24960784216491644 chrY 59373566 358817 0.006043379641371044 0.16095495004154803