BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524701.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 = 1,763,606 number of mapped reads = 1,623,206 (92.04%) number of supplementary alignments = 6,185 (0.35%) number of secondary alignments = 0 number of mapped bases = 95,669,286 bp number of sequenced bases = 95,640,249 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,940 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7575 >>>>>>> ACTG content number of A's = 24,928,062 bp (26.06%) number of C's = 18,658,589 bp (19.51%) number of T's = 29,917,972 bp (31.28%) number of G's = 22,122,889 bp (23.13%) number of N's = 12,737 bp (0.01%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 482,247 number of insertions = 6,179 mapped reads with insertion percentage = 0.38% number of deletions = 18,054 mapped reads with deletion percentage = 1.1% homopolymer indels = 44.47% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.3003X There is a 2.78% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 7744669 0.03107181426039456 0.5567458416664991 chr2 243199373 8131096 0.03343386909143059 0.41533376725539417 chr3 198022430 6358475 0.03210987260382574 0.19580895590885813 chr4 191154276 6117559 0.03200325479509546 0.22480945182024234 chr5 180915260 5689838 0.031450293358338044 0.19560891852872056 chr6 171115067 5560122 0.032493468269512465 0.22139538152666324 chr7 159138663 5230571 0.032868008951413646 0.34114025950463334 chr8 146364022 4844491 0.033098919623840345 0.3184633002176164 chr9 141213431 4013141 0.028418975246058572 0.2415462656737248 chr10 135534747 4678516 0.03451894147852727 0.318310651773427 chr11 135006516 4330590 0.032076896199587875 0.24797587112782438 chr12 133851895 4277978 0.03196053369285508 0.19672182800891927 chr13 115169878 2966689 0.02575924409679413 0.17734826544702906 chr14 107349540 2879401 0.02682266733513716 0.1846482210371296 chr15 102531392 2768065 0.026997243927011152 0.17965839143380477 chr16 90354753 2801159 0.03100178913664896 0.21273960837579167 chr17 81195210 2624654 0.03232523199336513 0.20690991867290157 chr18 78077248 2560645 0.03279630193933065 0.43336899045932853 chr19 59128983 1991833 0.03368623810086502 0.4079772846691318 chr20 63025520 2045601 0.032456709599539994 0.2003367756295704 chr21 48129895 1301235 0.02703589941345187 0.2028128976413454 chr22 51304566 1126163 0.021950541400155302 0.1608540969736579 chrMT 16571 21301 1.2854384165107717 1.2726361043315042 chrX 155270560 5278854 0.03399777781441633 0.22093058853149372 chrY 59373566 326640 0.005501438131575253 0.19807560561035586