BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238073.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 = 1,428,598 number of mapped reads = 1,176,780 (82.37%) number of supplementary alignments = 14,249 (1%) number of secondary alignments = 0 number of mapped bases = 76,510,182 bp number of sequenced bases = 76,465,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,438 duplication rate = 7.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0628 >>>>>>> ACTG content number of A's = 20,571,507 bp (26.9%) number of C's = 14,399,548 bp (18.83%) number of T's = 23,967,672 bp (31.34%) number of G's = 17,523,054 bp (22.92%) number of N's = 4,211 bp (0.01%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 600,279 number of insertions = 4,900 mapped reads with insertion percentage = 0.41% number of deletions = 25,279 mapped reads with deletion percentage = 2.12% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2648X There is a 1.52% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% 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% 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 3104357 0.012454761346412052 0.2606608289921174 chr2 243199373 9433358 0.038788578620225306 0.3535518384593542 chr3 198022430 4680286 0.023635130626363892 0.2363016532108336 chr4 191154276 2960768 0.01548889233322722 0.1843872967459762 chr5 180915260 8078508 0.04465354663835433 0.33466467523295196 chr6 171115067 2604243 0.015219250096778445 0.20156723390487788 chr7 159138663 5863890 0.03684767667050213 0.35022658670962714 chr8 146364022 2845396 0.019440542567216414 0.2367045018748604 chr9 141213431 3630677 0.025710564315939606 0.2557216020364102 chr10 135534747 2182724 0.01610453443352058 0.22281871349574217 chr11 135006516 4097401 0.030349653641902737 0.2970370346674689 chr12 133851895 2386824 0.017831828230747124 0.19724077647058721 chr13 115169878 5187854 0.04504523309471596 0.34248982142985246 chr14 107349540 2230171 0.02077485380934096 0.22415541728744015 chr15 102531392 1161764 0.01133081271343707 0.15904268731221008 chr16 90354753 1357060 0.015019243093941056 0.17754102487786017 chr17 81195210 3484632 0.042916718855705895 0.3384990408815132 chr18 78077248 2009305 0.02573483378922372 0.28804217269849863 chr19 59128983 1685937 0.028512869906793425 0.3019779912887497 chr20 63025520 949275 0.015061755936325475 0.1802199585974071 chr21 48129895 1023607 0.021267592626163012 0.23566150713699346 chr22 51304566 511909 0.00997784485692755 0.14877613088069805 chrMT 16571 57422 3.465210307163116 3.4989498520027214 chrX 155270560 4787178 0.030831201999915504 0.27297200488858864 chrY 59373566 195636 0.003295001684756479 0.08146219986577759