BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524899.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 = 685,355 number of mapped reads = 633,171 (92.39%) number of supplementary alignments = 2,266 (0.33%) number of secondary alignments = 0 number of mapped bases = 37,255,176 bp number of sequenced bases = 37,243,615 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,490 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2854 >>>>>>> ACTG content number of A's = 10,068,068 bp (27.03%) number of C's = 6,916,356 bp (18.57%) number of T's = 11,355,668 bp (30.49%) number of G's = 8,898,288 bp (23.89%) number of N's = 5,235 bp (0.01%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 181,737 number of insertions = 3,238 mapped reads with insertion percentage = 0.51% number of deletions = 7,241 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.45% >>>>>>> Coverage mean coverageData = 0.012X std coverageData = 0.1461X There is a 1.14% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2981389 0.011961410519414514 0.2461142900324091 chr2 243199373 3143398 0.012925189572754367 0.15525082067492235 chr3 198022430 2489639 0.012572510093932288 0.11592875017068785 chr4 191154276 2415807 0.01263799612832098 0.12115673554122815 chr5 180915260 2249808 0.012435700559477405 0.11552085405959353 chr6 171115067 2158603 0.012614920695440571 0.12121011920649538 chr7 159138663 2076468 0.013048167936411531 0.18426274824711428 chr8 146364022 1877517 0.012827722102362013 0.1405437847742511 chr9 141213431 1573034 0.011139407837204946 0.13197698695549548 chr10 135534747 1786861 0.013183785262092237 0.14306529252224595 chr11 135006516 1700415 0.012595058745164566 0.14060460260700855 chr12 133851895 1664748 0.01243723893486902 0.11647924156866894 chr13 115169878 1193180 0.010360174211524301 0.10527517450313771 chr14 107349540 1132460 0.010549276689960665 0.1079028963244708 chr15 102531392 1052349 0.01026367612369878 0.10481545007933851 chr16 90354753 1082015 0.011975186297061761 0.1192733633082957 chr17 81195210 974721 0.012004661358718083 0.11733412738423596 chr18 78077248 1012200 0.01296408398000913 0.2308275497491011 chr19 59128983 726327 0.012283772917251088 0.173820685348061 chr20 63025520 785594 0.012464696840264071 0.11609159996904685 chr21 48129895 495017 0.010285021398862391 0.11073087253578148 chr22 51304566 437047 0.00851867648583169 0.09566943065562436 chrMT 16571 5830 0.3518194436063002 0.586302930881799 chrX 155270560 2127026 0.013698836405304393 0.1291545514123995 chrY 59373566 113723 0.001915380996317452 0.060680311892822816