BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524927.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 = 3,348,831 number of mapped reads = 3,087,303 (92.19%) number of supplementary alignments = 11,615 (0.35%) number of secondary alignments = 0 number of mapped bases = 179,007,468 bp number of sequenced bases = 178,951,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 338,715 duplication rate = 8.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6771 >>>>>>> ACTG content number of A's = 45,126,004 bp (25.22%) number of C's = 33,498,830 bp (18.72%) number of T's = 57,633,034 bp (32.21%) number of G's = 42,692,540 bp (23.86%) number of N's = 1,433 bp (0%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 917,853 number of insertions = 13,488 mapped reads with insertion percentage = 0.43% number of deletions = 33,279 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.9% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.5052X There is a 4.34% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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% 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 18681471 0.07495054947124886 0.9877032697853992 chr2 243199373 15891144 0.0653420434599558 0.6616248680532512 chr3 198022430 11189279 0.056505109042445344 0.30551823519814764 chr4 191154276 8010021 0.0419034361543657 0.37852668573197157 chr5 180915260 11188420 0.06184342879644315 0.32013848826645636 chr6 171115067 11717052 0.06847469486716795 0.36651216738378234 chr7 159138663 10630184 0.06679824877000506 0.5653596725573513 chr8 146364022 15576441 0.10642260841943794 0.6236659552641813 chr9 141213431 6466000 0.045788845679983516 0.3895059843362028 chr10 135534747 7803266 0.0575739149754712 0.5795145985016649 chr11 135006516 8901271 0.0659321584152279 0.4156624924278879 chr12 133851895 5542523 0.0414078784614891 0.27759325019827796 chr13 115169878 4182783 0.03631837658107096 0.2465190116918066 chr14 107349540 3353710 0.03124102814040936 0.2432230546569429 chr15 102531392 4688982 0.04573215976624993 0.2773476197021885 chr16 90354753 5442934 0.060239598020925364 0.34818276421456706 chr17 81195210 4256691 0.052425395537495374 0.3097434827184181 chr18 78077248 4667091 0.05977530099421537 0.6704411446826068 chr19 59128983 3806664 0.06437898652848469 0.6528593862983507 chr20 63025520 3461110 0.054916008626346914 0.3226023442544682 chr21 48129895 1564449 0.0325047249739481 0.33491494247046205 chr22 51304566 3486711 0.06796102709454749 0.3435085054418053 chrMT 16571 36782 2.2196608532979303 2.250200389396535 chrX 155270560 7905115 0.05091187279803718 0.3336760647493777 chrY 59373566 557374 0.009387578303785896 0.366980378967852