BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525017.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 = 1,656,385 number of mapped reads = 1,508,365 (91.06%) number of supplementary alignments = 5,054 (0.31%) number of secondary alignments = 0 number of mapped bases = 86,354,361 bp number of sequenced bases = 86,326,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,079 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6922 >>>>>>> ACTG content number of A's = 20,864,144 bp (24.17%) number of C's = 15,991,831 bp (18.52%) number of T's = 27,847,024 bp (32.26%) number of G's = 21,622,881 bp (25.05%) number of N's = 778 bp (0%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 424,647 number of insertions = 5,051 mapped reads with insertion percentage = 0.33% number of deletions = 16,601 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.8% >>>>>>> Coverage mean coverageData = 0.0279X std coverageData = 0.258X There is a 2.54% of reference with a coverageData >= 1X There is a 0.17% 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 9017808 0.03617968117319154 0.482112708901942 chr2 243199373 8080611 0.03322628220756145 0.3069583704224027 chr3 198022430 4627134 0.023366716588620794 0.16550176717261603 chr4 191154276 5463634 0.028582326874027134 0.19724562898626344 chr5 180915260 3660164 0.020231372411592036 0.15568996671239016 chr6 171115067 6943198 0.040576193094673536 0.2926878079043006 chr7 159138663 5355947 0.03365585018142323 0.3349103284348541 chr8 146364022 5945380 0.040620501669460816 0.26090825925782263 chr9 141213431 2364038 0.01674088635379166 0.19174895599417235 chr10 135534747 4368253 0.032229764666916 0.2536670954700103 chr11 135006516 3570827 0.026449293751125317 0.2235765798098599 chr12 133851895 3800519 0.028393464283789183 0.18406539713699882 chr13 115169878 1647622 0.014306014980757382 0.1287582131375582 chr14 107349540 1983498 0.018477005118047084 0.1533281251946277 chr15 102531392 2378310 0.02319592032847852 0.17706935775719063 chr16 90354753 2763724 0.030587477783266145 0.19730264079781237 chr17 81195210 2238207 0.027565751723531474 0.23392178371175973 chr18 78077248 1680343 0.02152154491920617 0.3027594212645599 chr19 59128983 2136319 0.03612981133127218 0.3094738602277282 chr20 63025520 2079172 0.03298936684695342 0.19697968945531066 chr21 48129895 1228343 0.025521414497164392 0.1806242990735356 chr22 51304566 1153667 0.02248663403565289 0.15926514620225887 chrMT 16571 10864 0.6556031621507453 0.9223732504763511 chrX 155270560 3620389 0.023316648049701114 0.19210899983814622 chrY 59373566 236390 0.003981401420288618 0.10143032868014451