BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926938.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 12,291,528 number of mapped reads = 12,028,689 (97.86%) number of supplementary alignments = 398,584 (3.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,030,141 number of mapped paired reads (second in pair) = 5,998,548 number of mapped paired reads (both in pair) = 11,870,002 number of mapped paired reads (singletons) = 158,687 number of mapped bases = 1,103,065,629 bp number of sequenced bases = 1,102,236,757 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 687,710 duplication rate = 4.53% >>>>>>> Insert size mean insert size = 353,865.6015 std insert size = 5,849,741.6669 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.7444 >>>>>>> ACTG content number of A's = 313,602,513 bp (28.45%) number of C's = 216,932,579 bp (19.68%) number of T's = 318,759,393 bp (28.92%) number of G's = 252,718,254 bp (22.93%) number of N's = 224,018 bp (0.02%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 10,023,940 number of insertions = 184,509 mapped reads with insertion percentage = 1.51% number of deletions = 568,344 mapped reads with deletion percentage = 4.61% homopolymer indels = 52.19% >>>>>>> Coverage mean coverageData = 0.3563X std coverageData = 1.5616X There is a 20.63% of reference with a coverageData >= 1X There is a 8.17% of reference with a coverageData >= 2X There is a 3.31% of reference with a coverageData >= 3X There is a 1.49% of reference with a coverageData >= 4X There is a 0.71% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 95026329 0.3812481133196455 1.8615494990622528 chr2 243199373 98499426 0.4050151313506881 2.7434960593147766 chr3 198022430 72655328 0.36690453702643683 0.8954398842699025 chr4 191154276 66405505 0.34739220272530025 1.1505737863299434 chr5 180915260 62835362 0.34731930297090474 0.8520729417671307 chr6 171115067 66086293 0.38620966673846435 1.0463367261117829 chr7 159138663 59338487 0.37287285114365953 1.1593342668545314 chr8 146364022 57762654 0.39465063347329987 1.0665932455595326 chr9 141213431 45478793 0.32205713491941146 1.576832461159929 chr10 135534747 56213003 0.41474975417189514 3.369174322079916 chr11 135006516 51397619 0.38070472835548175 1.5760818648628205 chr12 133851895 49287057 0.3682208384124857 0.9128847988358659 chr13 115169878 31748353 0.275665421821494 0.7594981600483606 chr14 107349540 32487114 0.3026292800136824 0.8354477893523571 chr15 102531392 32892604 0.3208052027617064 0.8703046908371355 chr16 90354753 36506048 0.404030189756592 2.1205219541932907 chr17 81195210 26649066 0.32820982912661967 1.087420578372719 chr18 78077248 29903633 0.38300060217286347 1.5638815043458054 chr19 59128983 18045554 0.3051896563145691 1.4430315400377558 chr20 63025520 25048898 0.3974405605856167 0.9643083334276457 chr21 48129895 13245265 0.27519829411636987 1.0191151481917768 chr22 51304566 12601725 0.2456257986862222 0.7726510913777098 chrMT 16571 203231 12.26425683422847 10.84593768584411 chrX 155270560 61020906 0.39299726876749846 1.0214962000667616 chrY 59373566 1727376 0.029093351071417875 0.9671109764290802