BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008737.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 = 1,526,733 number of mapped reads = 1,103,422 (72.27%) number of supplementary alignments = 4,375 (0.29%) number of secondary alignments = 0 number of mapped bases = 71,242,424 bp number of sequenced bases = 71,199,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,773 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4805 >>>>>>> ACTG content number of A's = 20,068,403 bp (28.19%) number of C's = 12,119,774 bp (17.02%) number of T's = 21,931,564 bp (30.8%) number of G's = 17,075,852 bp (23.98%) number of N's = 3,494 bp (0%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 673,872 number of insertions = 5,869 mapped reads with insertion percentage = 0.53% number of deletions = 27,023 mapped reads with deletion percentage = 2.42% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.023X std coverageData = 0.2309X There is a 2.11% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% 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 6028161 0.024185139342140297 0.37236432449729384 chr2 243199373 6007991 0.02470397405177521 0.29356200338543426 chr3 198022430 5545559 0.02800470128560689 0.18360655689199368 chr4 191154276 3855620 0.020170200116266298 0.15533259210767816 chr5 180915260 3462493 0.01913875590151986 0.1491278465164939 chr6 171115067 4260930 0.024900963279872953 0.19168904629338798 chr7 159138663 3882335 0.02439592570914084 0.30635360710360005 chr8 146364022 5666417 0.03871454830614043 0.25084869835827633 chr9 141213431 2456934 0.017398727462404055 0.22115594440598413 chr10 135534747 4145632 0.030587226462303427 0.2901780577751437 chr11 135006516 3128558 0.023173385201644636 0.21984300151563294 chr12 133851895 3318269 0.024790601582443044 0.17184174896441934 chr13 115169878 1530176 0.013286251809696281 0.12583934738545982 chr14 107349540 2508057 0.023363462945439728 0.171011411412959 chr15 102531392 1753696 0.01710399094162303 0.14191889155942805 chr16 90354753 1727773 0.019122104179732525 0.16221047039544254 chr17 81195210 2123463 0.026152564911156705 0.20088020160601575 chr18 78077248 1363405 0.017462257378743677 0.3351026627515946 chr19 59128983 1330385 0.022499710505759926 0.2585130172369032 chr20 63025520 1566843 0.024860453352864045 0.17151493430957154 chr21 48129895 778415 0.016173212096141077 0.14066314944343886 chr22 51304566 745231 0.014525627212205634 0.12819817651400103 chrMT 16571 14913 0.8999456882505582 1.1636299715479255 chrX 155270560 3854472 0.024824229396738184 0.1869157443674003 chrY 59373566 186696 0.003144429627150911 0.07919149513030531