BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238673.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 = 3,619,276 number of mapped reads = 3,225,418 (89.12%) number of supplementary alignments = 27,652 (0.76%) number of secondary alignments = 0 number of mapped bases = 199,550,398 bp number of sequenced bases = 199,456,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,118,703 duplication rate = 20.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.0154 >>>>>>> ACTG content number of A's = 50,251,612 bp (25.19%) number of C's = 35,164,258 bp (17.63%) number of T's = 66,981,927 bp (33.58%) number of G's = 47,048,880 bp (23.59%) number of N's = 10,202 bp (0.01%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,154,500 number of insertions = 12,228 mapped reads with insertion percentage = 0.38% number of deletions = 56,377 mapped reads with deletion percentage = 1.73% homopolymer indels = 41.72% >>>>>>> Coverage mean coverageData = 0.0645X std coverageData = 1.0226X There is a 2.21% of reference with a coverageData >= 1X There is a 1.19% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 13550799 0.05436615943275824 0.6600103570963066 chr2 243199373 22917508 0.09423341728763421 2.3973714328051767 chr3 198022430 3205901 0.016189585189920152 0.2982441073387147 chr4 191154276 14283619 0.07472298971747825 0.6596881723650702 chr5 180915260 8057685 0.04453844855320662 0.5137162852325804 chr6 171115067 11736325 0.06858732667883653 0.9317600678409607 chr7 159138663 25851274 0.16244496159930663 1.7491657819272062 chr8 146364022 7316714 0.04998983971621113 0.7010861394425715 chr9 141213431 2098546 0.014860810229871122 0.4010088196883918 chr10 135534747 5202381 0.03838411267333535 0.5316741563598677 chr11 135006516 3252970 0.024094911093031985 0.3855828779728255 chr12 133851895 9884653 0.07384768814815808 0.6675327977425052 chr13 115169878 7111529 0.06174816821460903 0.7376167226246909 chr14 107349540 9031693 0.08413350443793238 0.7182255021825438 chr15 102531392 6196201 0.06043223328129594 0.7260245893181534 chr16 90354753 3324342 0.036792109873843605 0.4956474756139293 chr17 81195210 1152810 0.014198005030099683 0.2564399609273472 chr18 78077248 16594843 0.2125439026744385 2.0932267379369187 chr19 59128983 1339230 0.022649298737304514 0.48727471157468555 chr20 63025520 851933 0.013517270464408704 0.27771943934166193 chr21 48129895 2783264 0.0578281751913234 0.5883729027182817 chr22 51304566 979071 0.019083506134717133 0.31561498310762043 chrMT 16571 99499 6.004405286343612 6.665943432243291 chrX 155270560 22270963 0.14343326255795047 0.9414676487403243 chrY 59373566 456645 0.007691048908869648 0.32999785596296904