BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230343.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 = 3,040,335 number of mapped reads = 2,869,753 (94.39%) number of supplementary alignments = 25,082 (0.82%) number of secondary alignments = 0 number of mapped bases = 205,874,925 bp number of sequenced bases = 205,770,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,797 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4237 >>>>>>> ACTG content number of A's = 62,600,686 bp (30.42%) number of C's = 40,642,839 bp (19.75%) number of T's = 61,095,013 bp (29.69%) number of G's = 41,313,775 bp (20.08%) number of N's = 118,286 bp (0.06%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,876,916 number of insertions = 17,949 mapped reads with insertion percentage = 0.62% number of deletions = 61,244 mapped reads with deletion percentage = 2.11% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0665X std coverageData = 0.7078X There is a 5.24% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 21011836 0.08430003470282227 1.7042628723811992 chr2 243199373 15092200 0.06205690341150674 0.5500442652329903 chr3 198022430 14618847 0.07382419759216166 0.35072084357459443 chr4 191154276 18450921 0.09652371574465853 0.40995591215500243 chr5 180915260 12557592 0.06941145816002475 0.32111044688637536 chr6 171115067 11633906 0.06798878791895047 0.4104409531730958 chr7 159138663 11296934 0.07098799114580974 0.751046816699741 chr8 146364022 9621184 0.065734624319083 0.6324478460443265 chr9 141213431 6295775 0.04458340085228862 0.5508525788029656 chr10 135534747 10820801 0.07983783671356247 0.8554706160607427 chr11 135006516 10463841 0.07750619236778171 0.731646004016569 chr12 133851895 8890352 0.06641932114595762 0.32878588993608265 chr13 115169878 2071971 0.017990563470076784 0.15660668213502374 chr14 107349540 5652953 0.05265931274600711 0.3230793476865266 chr15 102531392 5099489 0.04973587991470944 0.26453024934848296 chr16 90354753 5752743 0.06366840491501316 0.4350669772612057 chr17 81195210 5114989 0.06299619152410592 0.3702883874510932 chr18 78077248 5072259 0.06496462324081914 1.1129768187515783 chr19 59128983 4165473 0.07044722889957367 1.111405744108868 chr20 63025520 1741533 0.027632187723322234 0.2183057611009286 chr21 48129895 1820452 0.03782372681261823 0.32799803599441213 chr22 51304566 1497602 0.02919042332411505 0.20040904309011606 chrMT 16571 2230 0.13457244583911654 0.38214190153873345 chrX 155270560 16480609 0.106141235015833 0.48549688915878736 chrY 59373566 648433 0.010921240607309994 0.28674886262155597