BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524622.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 = 3,201,922 number of mapped reads = 2,928,335 (91.46%) number of supplementary alignments = 10,872 (0.34%) number of secondary alignments = 0 number of mapped bases = 168,430,845 bp number of sequenced bases = 168,387,498 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,809 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9181 >>>>>>> ACTG content number of A's = 43,521,712 bp (25.85%) number of C's = 33,059,373 bp (19.63%) number of T's = 52,435,684 bp (31.14%) number of G's = 39,365,981 bp (23.38%) number of N's = 4,748 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 809,943 number of insertions = 9,013 mapped reads with insertion percentage = 0.31% number of deletions = 25,902 mapped reads with deletion percentage = 0.88% homopolymer indels = 43.75% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.4544X There is a 4.63% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% 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% 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 12149751 0.048745118271942035 0.8004028211306086 chr2 243199373 14445901 0.05939941711938542 0.5281961260812574 chr3 198022430 10194043 0.05147923394334672 0.25706887596783934 chr4 191154276 10398379 0.05439783622732039 0.32031482743964634 chr5 180915260 9368374 0.051783216075857834 0.26314522047660865 chr6 171115067 8888921 0.051947038655573215 0.2988137459915897 chr7 159138663 10777846 0.06772613139272132 0.6454044309907302 chr8 146364022 7418013 0.0506819428616139 0.4346754437365028 chr9 141213431 7971529 0.056450218251548605 0.48128051566520463 chr10 135534747 6537694 0.048236294711938334 0.4331580194528437 chr11 135006516 6219719 0.04606976895841087 0.37987292766523917 chr12 133851895 11393094 0.08511716625304408 0.38522346758727166 chr13 115169878 6423421 0.05577344624781143 0.26719897292075834 chr14 107349540 5989581 0.05579512497212377 0.30996686290389897 chr15 102531392 4350560 0.042431492591069084 0.2400489164196433 chr16 90354753 4853000 0.05371051149904643 0.30523665548324036 chr17 81195210 4613526 0.05682017449058879 0.2873035537381314 chr18 78077248 5424359 0.0694742596460367 0.8849836449155352 chr19 59128983 2890667 0.04888748044254372 0.6271555024020932 chr20 63025520 4974786 0.07893288306070304 0.33786538002500477 chr21 48129895 2033157 0.04224312145289326 0.2860114550636866 chr22 51304566 1704509 0.03322333922481675 0.20396671846518696 chrMT 16571 2381 0.1436847504676845 0.3908066862003586 chrX 155270560 8927863 0.05749874927996653 0.35757971750147677 chrY 59373566 479771 0.008080548842223827 0.18945771984349635