BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240218.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 = 3,315,257 number of mapped reads = 2,918,853 (88.04%) number of supplementary alignments = 24,821 (0.75%) number of secondary alignments = 0 number of mapped bases = 197,687,352 bp number of sequenced bases = 197,611,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 226,589 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.043 >>>>>>> ACTG content number of A's = 56,135,615 bp (28.41%) number of C's = 36,422,666 bp (18.43%) number of T's = 62,918,462 bp (31.84%) number of G's = 42,115,934 bp (21.31%) number of N's = 19,284 bp (0.01%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,492,768 number of insertions = 13,920 mapped reads with insertion percentage = 0.47% number of deletions = 43,311 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.22% >>>>>>> Coverage mean coverageData = 0.0639X std coverageData = 0.6392X There is a 4.41% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% 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 0.01% 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 18143298 0.07279138534222548 1.2108265290943612 chr2 243199373 12913350 0.05309779314274794 0.6391442711000099 chr3 198022430 9867742 0.049831435762100286 0.3058678540258963 chr4 191154276 12584564 0.06583459320575177 0.3634400544864226 chr5 180915260 13421707 0.07418781035939147 0.37304184918983435 chr6 171115067 12375097 0.07232032349319654 0.4441414746090509 chr7 159138663 8627796 0.054215586818144874 0.657178358706492 chr8 146364022 14312342 0.0977859299329722 1.1160570776337881 chr9 141213431 6583480 0.04662077787770768 0.5033567016892657 chr10 135534747 14311037 0.10558943235419918 0.7892089297966257 chr11 135006516 10131760 0.07504645183199898 0.6912053602642853 chr12 133851895 8498120 0.0634889778736416 0.3542918736154742 chr13 115169878 7986641 0.06934661335666258 0.3591751429317243 chr14 107349540 5969501 0.05560807247054808 0.3503774075926906 chr15 102531392 4985754 0.04862660988743818 0.31266730679039356 chr16 90354753 5159487 0.057102552203313534 0.3560156587623002 chr17 81195210 4584752 0.05646579397971876 0.4007013530755217 chr18 78077248 7180635 0.09196834140465607 1.128591538352632 chr19 59128983 2825976 0.04779341461022592 0.8011389669050041 chr20 63025520 3113473 0.0494001953494394 0.3153741875204862 chr21 48129895 2425146 0.05038751902533758 0.3220000117693725 chr22 51304566 2000255 0.03898785538893361 0.2635261125677041 chrMT 16571 8057 0.48621085028061073 0.9600528910330947 chrX 155270560 9279053 0.059760543144817664 0.42315094238619877 chrY 59373566 398329 0.006708860976953953 0.1410742946407637