BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013281.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 = 2,474,589 number of mapped reads = 2,246,998 (90.8%) number of supplementary alignments = 12,167 (0.49%) number of secondary alignments = 0 number of mapped bases = 151,470,394 bp number of sequenced bases = 151,401,303 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,183 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.159 >>>>>>> ACTG content number of A's = 42,352,711 bp (27.97%) number of C's = 27,810,420 bp (18.37%) number of T's = 47,857,907 bp (31.61%) number of G's = 33,378,094 bp (22.05%) number of N's = 2,171 bp (0%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,046,759 number of insertions = 10,586 mapped reads with insertion percentage = 0.47% number of deletions = 40,237 mapped reads with deletion percentage = 1.77% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.0489X std coverageData = 0.4268X There is a 4.18% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12742518 0.051123314954549304 0.8072589482624662 chr2 243199373 19296196 0.0793431157406808 0.46536302310448163 chr3 198022430 10337386 0.052203106486472264 0.25789324755545967 chr4 191154276 8854996 0.0463238185684112 0.26304163792635127 chr5 180915260 8005886 0.044252132186085355 0.24161713079686425 chr6 171115067 8673218 0.05068646585049112 0.3343764535703637 chr7 159138663 10864674 0.06827174361770276 0.8129488395830863 chr8 146364022 8031786 0.054875411936958114 0.49001745025119464 chr9 141213431 4803976 0.03401925699262983 0.3443138214088266 chr10 135534747 7750282 0.05718298939238069 0.3739182700351534 chr11 135006516 4862057 0.03601349878549566 0.267279432563965 chr12 133851895 6901291 0.051559157978301316 0.26123422254840806 chr13 115169878 1621334 0.014077760853406479 0.13394759690097927 chr14 107349540 4817281 0.044874724195371495 0.25732140234503154 chr15 102531392 4811853 0.04693053421141498 0.26713484016837014 chr16 90354753 4616100 0.05108862397089393 0.2721358658515177 chr17 81195210 4331288 0.05334413199990492 0.30710679054487827 chr18 78077248 2944736 0.037715673585216526 0.5894731171410212 chr19 59128983 3442022 0.058212095411821985 0.5500687102538586 chr20 63025520 2771711 0.043977598280823385 0.24488081139215329 chr21 48129895 2857620 0.05937307779291852 0.2946333429819511 chr22 51304566 1041899 0.020308114486340262 0.15812555283465018 chrMT 16571 21806 1.3159133425864462 1.6263408513936233 chrX 155270560 6777988 0.04365275683941631 0.26687219737802303 chrY 59373566 290490 0.004892581321458779 0.12263682096831952