BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525006.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 = 1,652,577 number of mapped reads = 1,512,688 (91.54%) number of supplementary alignments = 5,180 (0.31%) number of secondary alignments = 0 number of mapped bases = 87,397,038 bp number of sequenced bases = 87,368,588 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,577 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1878 >>>>>>> ACTG content number of A's = 21,256,137 bp (24.33%) number of C's = 16,319,042 bp (18.68%) number of T's = 27,997,944 bp (32.05%) number of G's = 21,794,475 bp (24.95%) number of N's = 990 bp (0%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 431,622 number of insertions = 5,654 mapped reads with insertion percentage = 0.37% number of deletions = 16,859 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.9% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2581X There is a 2.57% of reference with a coverageData >= 1X There is a 0.18% 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 9442868 0.03788503299255571 0.49112143259167873 chr2 243199373 8368202 0.034408814039171065 0.3035431890994517 chr3 198022430 4802301 0.024251298198895953 0.16848585423850984 chr4 191154276 5599076 0.029290874978909705 0.19724795901948458 chr5 180915260 3785357 0.020923370422152338 0.157897380760758 chr6 171115067 5837934 0.034117007358563 0.2641292411413359 chr7 159138663 5540164 0.034813438139793845 0.3476300603298975 chr8 146364022 5325211 0.03638333333037268 0.25755919116126896 chr9 141213431 2396333 0.016969582730413227 0.18452274685792147 chr10 135534747 4425436 0.03265167123527371 0.254373015345576 chr11 135006516 3652053 0.02705093878579905 0.22325125235630347 chr12 133851895 4742682 0.03543231121232912 0.20338405896327677 chr13 115169878 1674375 0.014538306622153408 0.13034865333722825 chr14 107349540 1990850 0.018545491671412843 0.14998584042337024 chr15 102531392 2439907 0.023796682678413263 0.17786616907740058 chr16 90354753 2826926 0.03128696505871694 0.19856660483363334 chr17 81195210 2362448 0.02909590356376934 0.24489791290655488 chr18 78077248 1707519 0.021869610465778712 0.2845586054535547 chr19 59128983 2229616 0.03770766698287369 0.30908162098951575 chr20 63025520 2134064 0.033860315630874604 0.19903416321871042 chr21 48129895 1240785 0.025779923268064473 0.17978887036695634 chr22 51304566 933335 0.018192045518911515 0.14342631700431024 chrMT 16571 8707 0.525436002655241 0.783715728554071 chrX 155270560 3695127 0.023797988491830003 0.1882024836653498 chrY 59373566 235762 0.003970824322729748 0.10324730175273719