BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008753.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 = 1,196,128 number of mapped reads = 770,029 (64.38%) number of supplementary alignments = 3,048 (0.25%) number of secondary alignments = 0 number of mapped bases = 50,044,553 bp number of sequenced bases = 50,016,750 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,466 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6073 >>>>>>> ACTG content number of A's = 14,932,373 bp (29.85%) number of C's = 8,507,353 bp (17.01%) number of T's = 14,965,813 bp (29.92%) number of G's = 11,608,092 bp (23.21%) number of N's = 3,119 bp (0.01%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 555,097 number of insertions = 3,941 mapped reads with insertion percentage = 0.51% number of deletions = 18,368 mapped reads with deletion percentage = 2.35% homopolymer indels = 49.82% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 0.163X There is a 1.41% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 4135256 0.016590755053725623 0.20316116399294037 chr2 243199373 4313079 0.01773474555791721 0.1811911664472689 chr3 198022430 3876981 0.019578494214014037 0.1610268418691082 chr4 191154276 2911120 0.015229164949467308 0.14124421821805797 chr5 180915260 2816847 0.015569980111130482 0.14157544793600918 chr6 171115067 2819576 0.01647766061418776 0.15491830089249858 chr7 159138663 2784127 0.017494975435353506 0.1872563910870461 chr8 146364022 3646596 0.02491456541143697 0.21809397555945395 chr9 141213431 1781792 0.012617723309902441 0.15199838346801914 chr10 135534747 2560858 0.018894475820285406 0.17244167537806962 chr11 135006516 2184452 0.01618034495460945 0.1622589171573619 chr12 133851895 2320417 0.017335705258412666 0.151394952065259 chr13 115169878 1570254 0.01363424210625629 0.133847541412239 chr14 107349540 1698678 0.015823803250577508 0.14483766293378572 chr15 102531392 1387375 0.013531221735485655 0.13325039710787978 chr16 90354753 1223187 0.013537605487118094 0.13704913774331956 chr17 81195210 1210849 0.014912813206591867 0.14759494592401332 chr18 78077248 1072172 0.01373219506917047 0.2009656299751274 chr19 59128983 780407 0.013198383608255194 0.14538113458452476 chr20 63025520 1085981 0.017230813803678257 0.1495235576260282 chr21 48129895 589799 0.012254317197243002 0.1322420674973755 chr22 51304566 539972 0.010524833208802507 0.1169264456304676 chrMT 16571 18992 1.146098605998431 1.509011689070805 chrX 155270560 2603945 0.016770371666077588 0.15189170333661942 chrY 59373566 111841 0.0018836833886649153 0.05285270040265946