BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068148.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 = 4,065,573 number of mapped reads = 3,787,836 (93.17%) number of supplementary alignments = 30,653 (0.75%) number of secondary alignments = 0 number of mapped bases = 245,676,738 bp number of sequenced bases = 245,579,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 508,411 duplication rate = 11.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5314 >>>>>>> ACTG content number of A's = 65,714,696 bp (26.76%) number of C's = 43,987,054 bp (17.91%) number of T's = 80,088,754 bp (32.61%) number of G's = 55,760,102 bp (22.71%) number of N's = 28,820 bp (0.01%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,305,062 number of insertions = 15,908 mapped reads with insertion percentage = 0.42% number of deletions = 54,841 mapped reads with deletion percentage = 1.43% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0794X std coverageData = 0.6182X There is a 5.31% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 17187148 0.06895528657479252 0.9588665380374624 chr2 243199373 28603612 0.11761383940739024 0.9871560897793596 chr3 198022430 29259644 0.14775924121323025 0.5366800088797992 chr4 191154276 8515304 0.04454676179987729 0.3348283730705185 chr5 180915260 28959794 0.16007380471940288 0.5601620632049105 chr6 171115067 12722934 0.0743530901343714 0.5073232041099125 chr7 159138663 13557222 0.08519125236084206 0.5965170173524699 chr8 146364022 10703018 0.07312601726672967 0.8932303604596743 chr9 141213431 9738987 0.06896643563599839 0.4811963810163639 chr10 135534747 6646553 0.049039476201626735 0.5244812681586616 chr11 135006516 9596989 0.0710853763532421 0.5375810060673627 chr12 133851895 8895901 0.06646077741372283 0.3701295204276628 chr13 115169878 4070371 0.03534232275560802 0.2864860363266056 chr14 107349540 7962827 0.07417662898229466 0.3884883519770656 chr15 102531392 4364697 0.042569372314773604 0.32877145655157575 chr16 90354753 6763874 0.07485908350609956 0.40756498559357673 chr17 81195210 5706920 0.07028641221569598 0.42372337844007485 chr18 78077248 7782595 0.09967814183204818 1.0514528507820988 chr19 59128983 2518705 0.04259679216874067 0.7019081914315309 chr20 63025520 6054540 0.09606489561688662 0.4407591305877908 chr21 48129895 3761077 0.07814430095889467 0.4155595722559681 chr22 51304566 1387668 0.02704765108041261 0.22373236749573777 chrMT 16571 139894 8.442097640456218 5.844306467191812 chrX 155270560 10078937 0.06491209280110795 0.3843606681958746 chrY 59373566 697527 0.01174810689322585 0.24822733210373218