BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013251.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 = 1,387,093 number of mapped reads = 1,069,474 (77.1%) number of supplementary alignments = 5,692 (0.41%) number of secondary alignments = 0 number of mapped bases = 69,212,097 bp number of sequenced bases = 69,179,521 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,153 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.4955 >>>>>>> ACTG content number of A's = 21,054,106 bp (30.43%) number of C's = 11,368,830 bp (16.43%) number of T's = 21,749,851 bp (31.44%) number of G's = 14,981,088 bp (21.66%) number of N's = 25,646 bp (0.04%) GC percentage = 38.09% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 725,517 number of insertions = 4,335 mapped reads with insertion percentage = 0.4% number of deletions = 19,945 mapped reads with deletion percentage = 1.85% homopolymer indels = 49.76% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.1866X There is a 1.96% of reference with a coverageData >= 1X There is a 0.22% 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 4959532 0.019897771889603438 0.2346151288052485 chr2 243199373 8213253 0.0337716865742084 0.21852981970289723 chr3 198022430 4621300 0.023337255279616557 0.1703370661010351 chr4 191154276 4527757 0.023686401867358698 0.17321938480189902 chr5 180915260 3595681 0.019874945872448792 0.1578994356976922 chr6 171115067 3522583 0.020586048100603556 0.1717193695834125 chr7 159138663 4313700 0.02710654921111157 0.2374708599237071 chr8 146364022 4442238 0.03035061444266679 0.25314105540447246 chr9 141213431 2335029 0.016535459718417293 0.1528719191408049 chr10 135534747 3288202 0.024260952064196498 0.1873433424026143 chr11 135006516 3162145 0.02342216578642767 0.18103593114388672 chr12 133851895 3452161 0.025790901204648616 0.1802491367273027 chr13 115169878 1513639 0.013142663917730293 0.12711064715248072 chr14 107349540 2491084 0.023205353278644696 0.1719573169929018 chr15 102531392 1778641 0.017347282284044287 0.14754478543379626 chr16 90354753 2030516 0.022472708214918147 0.16982494216855237 chr17 81195210 1584379 0.01951320773725445 0.16107879369179928 chr18 78077248 1595888 0.020439859765549115 0.2162911748833424 chr19 59128983 975458 0.016497121217187178 0.16549567248667962 chr20 63025520 1398213 0.02218487050959675 0.16791338577721432 chr21 48129895 1316302 0.027348948091409715 0.1897585075249563 chr22 51304566 532163 0.010372624534042448 0.11279666663862853 chrMT 16571 9419 0.5684026311025285 0.9549140764637349 chrX 155270560 3450035 0.022219505101289002 0.17149223370442496 chrY 59373566 102779 0.0017310565445909044 0.04556567745921404