BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716826.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 788,731 number of mapped reads = 648,402 (82.21%) number of supplementary alignments = 781 (0.1%) number of secondary alignments = 0 number of mapped bases = 34,403,899 bp number of sequenced bases = 34,395,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,074 duplication rate = 7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3012 >>>>>>> ACTG content number of A's = 6,809,414 bp (19.8%) number of C's = 6,062,427 bp (17.63%) number of T's = 11,396,178 bp (33.13%) number of G's = 10,127,002 bp (29.44%) number of N's = 577 bp (0%) GC percentage = 47.07% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 215,288 number of insertions = 1,690 mapped reads with insertion percentage = 0.26% number of deletions = 4,807 mapped reads with deletion percentage = 0.74% homopolymer indels = 41.9% >>>>>>> Coverage mean coverageData = 0.0111X std coverageData = 0.1303X There is a 0.96% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 3400630 0.013643416358830256 0.14310370994561478 chr2 243199373 3240431 0.013324174976388612 0.17671917601235893 chr3 198022430 2427248 0.012257439725388685 0.12804896072378028 chr4 191154276 2091744 0.010942700544140586 0.12048278912314894 chr5 180915260 2014486 0.01113497004066987 0.12163738599651755 chr6 171115067 1537971 0.00898793441725386 0.11759150061531567 chr7 159138663 1950501 0.0122566129640036 0.13743472994492933 chr8 146364022 2250020 0.015372766949517143 0.14643606502594994 chr9 141213431 1644993 0.011648984012009452 0.12978667251998308 chr10 135534747 1652662 0.01219364064626173 0.13593783983862925 chr11 135006516 1326689 0.009826851616554567 0.12192335512910593 chr12 133851895 1403984 0.010489085716716973 0.11740229743901708 chr13 115169878 618754 0.005372533259087068 0.08744264842325934 chr14 107349540 1158131 0.01078841138955975 0.11990597986368208 chr15 102531392 635718 0.006200227926292077 0.09092044543764222 chr16 90354753 830417 0.009190628853802523 0.11695949009920312 chr17 81195210 1372112 0.016898927904737238 0.15451578541233194 chr18 78077248 935083 0.01197638267168433 0.13705855726759716 chr19 59128983 909902 0.015388426349223697 0.17088149474189898 chr20 63025520 965992 0.015326997698709982 0.14808001947637853 chr21 48129895 468630 0.00973677586456401 0.11917824569568514 chr22 51304566 396712 0.007732489151160542 0.104572585752139 chrMT 16571 1575 0.09504556152314284 0.34970209238733047 chrX 155270560 1079686 0.006953578321608423 0.09736102628892801 chrY 59373566 89828 0.0015129291712072676 0.05059192744232092