BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237583.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 = 1,726,138 number of mapped reads = 1,400,278 (81.12%) number of supplementary alignments = 8,279 (0.48%) number of secondary alignments = 0 number of mapped bases = 88,104,622 bp number of sequenced bases = 88,051,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,020 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4472 >>>>>>> ACTG content number of A's = 22,490,170 bp (25.54%) number of C's = 16,684,902 bp (18.95%) number of T's = 26,647,992 bp (30.26%) number of G's = 22,212,458 bp (25.23%) number of N's = 15,646 bp (0.02%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 830,952 number of insertions = 8,305 mapped reads with insertion percentage = 0.59% number of deletions = 32,233 mapped reads with deletion percentage = 2.27% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2963X There is a 2.27% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 7687617 0.030842920146626235 0.36722534582316413 chr2 243199373 7510704 0.03088290856736707 0.4225304127179828 chr3 198022430 6267876 0.03165235372578753 0.23420749571106061 chr4 191154276 5533959 0.02895022343104687 0.2389817114011857 chr5 180915260 4737973 0.026188907447608344 0.20720104207302387 chr6 171115067 4564802 0.026676797549335617 0.233030849507262 chr7 159138663 5100409 0.03205009332018832 0.4219099539042791 chr8 146364022 4622445 0.03158183914896791 0.2840944121423664 chr9 141213431 3652769 0.02586700835843299 0.32297630029932184 chr10 135534747 3926634 0.02897141941025647 0.28665392411725016 chr11 135006516 3764677 0.027885150373038292 0.32544257356094514 chr12 133851895 5175001 0.038662142213227536 0.2723004743648192 chr13 115169878 2814489 0.02443771799428319 0.20766872850455276 chr14 107349540 2473408 0.02304069491122179 0.2389692874724175 chr15 102531392 2753438 0.026854585179142014 0.22482983185525773 chr16 90354753 2444009 0.027049036368900263 0.24494221424364887 chr17 81195210 2276060 0.02803194917532697 0.23806472269712456 chr18 78077248 2209404 0.02829766745877109 0.4432149250353647 chr19 59128983 1828802 0.030929028493522373 0.3167633755849551 chr20 63025520 1903746 0.03020595466725225 0.23723092281534255 chr21 48129895 1078686 0.022411974927433354 0.21494759465202287 chr22 51304566 1008390 0.019654975738416732 0.1873555046483732 chrMT 16571 78163 4.716854746243437 3.902840805154406 chrX 155270560 4365528 0.02811561959974898 0.23669180128567188 chrY 59373566 325633 0.005484477721954582 0.1377452816459124