BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237789.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,622,921 number of mapped reads = 2,379,762 (90.73%) number of supplementary alignments = 16,312 (0.62%) number of secondary alignments = 0 number of mapped bases = 154,428,725 bp number of sequenced bases = 154,348,656 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,503 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9972 >>>>>>> ACTG content number of A's = 39,764,428 bp (25.76%) number of C's = 30,427,666 bp (19.71%) number of T's = 45,838,321 bp (29.7%) number of G's = 38,281,027 bp (24.8%) number of N's = 37,214 bp (0.02%) GC percentage = 44.52% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,332,004 number of insertions = 14,155 mapped reads with insertion percentage = 0.59% number of deletions = 46,430 mapped reads with deletion percentage = 1.93% homopolymer indels = 43.97% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.5605X There is a 4.21% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 16388190 0.06574984621603008 1.068723958611937 chr2 243199373 13202293 0.054285884199216254 0.6372410245776746 chr3 198022430 9837827 0.04968036701700913 0.2871990193194108 chr4 191154276 5516863 0.028860787817270694 0.3622886745168688 chr5 180915260 6736800 0.037237323153392364 0.22162322475983076 chr6 171115067 9017599 0.052699035555998114 0.3390763044647734 chr7 159138663 8605785 0.054077273478161623 0.7599225792227046 chr8 146364022 7576528 0.05176496174722501 0.3807362684025055 chr9 141213431 6403190 0.04534405796003923 0.48137752065397765 chr10 135534747 9803831 0.07233444719530115 0.9856766270284584 chr11 135006516 7100955 0.0525971279786229 0.46227411124273815 chr12 133851895 6536974 0.04883736610527628 0.2557057943148598 chr13 115169878 5464612 0.04744827462611361 0.24452307875945703 chr14 107349540 4567880 0.042551463192110554 0.28987902947756483 chr15 102531392 2374043 0.023154303805804178 0.17373504529074343 chr16 90354753 4957854 0.05487098171802871 0.374907318659612 chr17 81195210 4431318 0.05457610122567575 0.3540957693189164 chr18 78077248 2247227 0.02878209795509186 0.8861202994479245 chr19 59128983 4028035 0.06812285271336393 0.8077328574619415 chr20 63025520 4160468 0.0660124343281896 0.3285645732215444 chr21 48129895 2010656 0.04177561575814782 0.3394160461463135 chr22 51304566 2195862 0.04280051798898367 0.23644274133596765 chrMT 16571 484930 29.263774063122323 20.074399518264546 chrX 155270560 10144149 0.06533208226981342 0.34427002372014 chrY 59373566 634856 0.01069256982139156 0.35263559177158366