BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524946.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 = 974,439 number of mapped reads = 906,840 (93.06%) number of supplementary alignments = 2,350 (0.24%) number of secondary alignments = 0 number of mapped bases = 53,281,389 bp number of sequenced bases = 53,263,577 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,414 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9339 >>>>>>> ACTG content number of A's = 12,997,652 bp (24.4%) number of C's = 9,902,021 bp (18.59%) number of T's = 16,887,949 bp (31.71%) number of G's = 13,475,327 bp (25.3%) number of N's = 628 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 255,561 number of insertions = 3,141 mapped reads with insertion percentage = 0.34% number of deletions = 10,399 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.183X There is a 1.61% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5778749 0.023184491885378293 0.32704913554043336 chr2 243199373 4460307 0.01834012540813582 0.20102904112713413 chr3 198022430 2975276 0.015024944396450442 0.12869084560092192 chr4 191154276 3525100 0.018441125533597794 0.14849084464286014 chr5 180915260 2373474 0.013119258154342535 0.12125627315164494 chr6 171115067 3990199 0.02331880570166273 0.20512738671780395 chr7 159138663 3449169 0.02167398503278867 0.24736786771105465 chr8 146364022 3153657 0.02154666807393418 0.18944487698586004 chr9 141213431 1499679 0.01061994591718404 0.14199630953247452 chr10 135534747 2777394 0.020492117788805848 0.17770166951496927 chr11 135006516 2282598 0.016907317273486266 0.1703608815600238 chr12 133851895 2492182 0.018618951939380464 0.1436689524903498 chr13 115169878 1041156 0.00904017628637238 0.09977860679209465 chr14 107349540 1245584 0.011603067884594568 0.11407076553764059 chr15 102531392 1734323 0.016915043931130868 0.14189304095813682 chr16 90354753 1699815 0.01881267939496221 0.14860661949182008 chr17 81195210 1307981 0.016109090671728048 0.15847229151286307 chr18 78077248 1117807 0.01431668032151953 0.20712231505679204 chr19 59128983 1266226 0.02141464195316872 0.21402866654074187 chr20 63025520 1178171 0.018693554610894128 0.14370217999758989 chr21 48129895 778576 0.01617655721044062 0.13655229399193433 chr22 51304566 697332 0.013592006606195636 0.12151119814030312 chrMT 16571 21243 1.2819383259911894 1.450783041006808 chrX 155270560 2294993 0.014780606188320567 0.14026823905877986 chrY 59373566 140398 0.002364655004888876 0.06428755420633048