BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716904.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 = 560,687 number of mapped reads = 481,789 (85.93%) number of supplementary alignments = 1,203 (0.21%) number of secondary alignments = 0 number of mapped bases = 26,806,979 bp number of sequenced bases = 26,799,253 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,725 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9531 >>>>>>> ACTG content number of A's = 6,015,270 bp (22.45%) number of C's = 5,002,556 bp (18.67%) number of T's = 8,697,136 bp (32.45%) number of G's = 7,083,552 bp (26.43%) number of N's = 739 bp (0%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 143,257 number of insertions = 2,061 mapped reads with insertion percentage = 0.43% number of deletions = 4,644 mapped reads with deletion percentage = 0.96% homopolymer indels = 40.3% >>>>>>> Coverage mean coverageData = 0.0087X std coverageData = 0.1068X There is a 0.82% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2129146 0.008542189349249404 0.1032846729922785 chr2 243199373 2119686 0.008715836615253115 0.14350740048084992 chr3 198022430 1764679 0.008911510680885998 0.10287325729027957 chr4 191154276 1644923 0.008605211635443614 0.10305059539977322 chr5 180915260 1511175 0.008352943803634917 0.09556957821773396 chr6 171115067 1441379 0.008423448766203621 0.09854182624927488 chr7 159138663 1495560 0.009397841931096279 0.1135505211237382 chr8 146364022 1299654 0.008879600206668276 0.10215421224512429 chr9 141213431 1224130 0.008668651355124995 0.1006381803178378 chr10 135534747 1371939 0.010122415324241539 0.1238410140422774 chr11 135006516 1348090 0.009985369891331763 0.11768412420590196 chr12 133851895 1211171 0.009048590608298821 0.09947348592948245 chr13 115169878 781634 0.006786791942247261 0.08580667357566536 chr14 107349540 805061 0.00749943595473255 0.09139241760888339 chr15 102531392 779652 0.007604032138761951 0.09340911323966575 chr16 90354753 901432 0.009976586400496274 0.108922157145043 chr17 81195210 825486 0.010166683478003197 0.10723935393701715 chr18 78077248 657557 0.00842187726698564 0.11310451153867436 chr19 59128983 683598 0.011561132380714208 0.12381581639691883 chr20 63025520 596292 0.00946111987651986 0.10245469776310007 chr21 48129895 348450 0.007239783091153637 0.09291409419555352 chr22 51304566 376632 0.007341100985046828 0.09025609468115948 chrMT 16571 2632 0.1588316939231187 0.3944239752581281 chrX 155270560 1395441 0.008987157642762414 0.1042877605733211 chrY 59373566 91580 0.0015424372522950703 0.055848116711338935