BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013320.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 = 1,999,901 number of mapped reads = 1,207,562 (60.38%) number of supplementary alignments = 13,865 (0.69%) number of secondary alignments = 0 number of mapped bases = 77,892,456 bp number of sequenced bases = 77,847,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,016 duplication rate = 9.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2707 >>>>>>> ACTG content number of A's = 20,765,992 bp (26.68%) number of C's = 14,941,883 bp (19.19%) number of T's = 24,066,776 bp (30.92%) number of G's = 18,064,340 bp (23.2%) number of N's = 8,831 bp (0.01%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 637,204 number of insertions = 5,006 mapped reads with insertion percentage = 0.41% number of deletions = 25,801 mapped reads with deletion percentage = 2.11% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0252X std coverageData = 0.3133X There is a 1.43% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% 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 16476114 0.06610259959994243 0.5813504018680793 chr2 243199373 3007028 0.012364456219218953 0.3116261320466692 chr3 198022430 3854984 0.01946741083825706 0.22298967392260458 chr4 191154276 5024456 0.026284821376425814 0.2558823491520868 chr5 180915260 2789022 0.015416178823168371 0.19852054958988183 chr6 171115067 3672858 0.021464258316890354 0.252872027304644 chr7 159138663 3493117 0.02195014670947688 0.45941244361197403 chr8 146364022 7373096 0.050375057334786824 0.39568515331777243 chr9 141213431 1318190 0.009334735305737314 0.16143506327008894 chr10 135534747 4625582 0.03412838480452544 0.3711868276058759 chr11 135006516 3651012 0.027043228046859605 0.2700914413251666 chr12 133851895 6558414 0.04899754314273996 0.36289970342170436 chr13 115169878 943826 0.008195076841185853 0.1473822049861212 chr14 107349540 897260 0.008358303165528236 0.14300360579553198 chr15 102531392 1317153 0.012846338807143084 0.17886860278395034 chr16 90354753 2301604 0.025472970968112768 0.25754074521656917 chr17 81195210 2979109 0.03669069887250738 0.3286783218975294 chr18 78077248 839828 0.010756372970522732 0.2013235529983493 chr19 59128983 1985414 0.033577678817848094 0.4021409630517498 chr20 63025520 868684 0.013783051690807152 0.19107470549304922 chr21 48129895 783863 0.016286405777531824 0.20943287935125118 chr22 51304566 1214527 0.023672883228366068 0.26285733922043275 chrMT 16571 27469 1.6576549393518798 2.3455795440276472 chrX 155270560 1758044 0.011322455460970837 0.1696891813012091 chrY 59373566 131802 0.0022198767714238354 0.06638835858977947