BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238042.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 = 2,056,629 number of mapped reads = 1,548,328 (75.28%) number of supplementary alignments = 15,178 (0.74%) number of secondary alignments = 0 number of mapped bases = 97,559,892 bp number of sequenced bases = 97,511,758 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 252,005 duplication rate = 12.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.508 >>>>>>> ACTG content number of A's = 25,677,948 bp (26.33%) number of C's = 17,505,339 bp (17.95%) number of T's = 31,179,199 bp (31.97%) number of G's = 22,970,880 bp (23.56%) number of N's = 178,392 bp (0.18%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 844,550 number of insertions = 7,777 mapped reads with insertion percentage = 0.5% number of deletions = 29,016 mapped reads with deletion percentage = 1.85% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.3861X There is a 1.66% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 8558522 0.034337013748102156 0.6000065045881345 chr2 243199373 8313770 0.03418499767267081 0.4493175566101915 chr3 198022430 5705903 0.028814427739322256 0.2974329907401468 chr4 191154276 6367951 0.03331314963626553 0.3513979431908428 chr5 180915260 7141326 0.03947332027160119 0.3526550452629666 chr6 171115067 5840894 0.034134305659945186 0.350163874231818 chr7 159138663 4983521 0.03131558922296589 0.3685856827024 chr8 146364022 4867941 0.03325913659300781 0.394984316857911 chr9 141213431 4066309 0.02879548334180762 0.3369570770335566 chr10 135534747 5136565 0.03789851026172646 0.5006169560024273 chr11 135006516 4812507 0.035646479463257906 0.40399506824663073 chr12 133851895 4689890 0.035037905141350446 0.3245154842228628 chr13 115169878 2852015 0.0247635497191375 0.2672701736078874 chr14 107349540 2777955 0.025877660956907685 0.2872838592354418 chr15 102531392 2359404 0.023011528020608556 0.25962816000486355 chr16 90354753 2558902 0.028320613083851826 0.30903930541072183 chr17 81195210 2317942 0.02854776778088264 0.31149605782643297 chr18 78077248 2347353 0.0300644945887437 0.5185813028635811 chr19 59128983 1836352 0.03105671545204828 0.4255925648954712 chr20 63025520 1931634 0.030648442091394088 0.3154430249608141 chr21 48129895 1462990 0.030396700429119988 0.3302456413605305 chr22 51304566 1315683 0.02564455958949151 0.26698368817158147 chrMT 16571 65674 3.963188703156116 3.772950045439973 chrX 155270560 4862930 0.03131907297816147 0.32436185170209597 chrY 59373566 385959 0.006500519103063474 0.22900449929306102