BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524642.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 = 1,105,434 number of mapped reads = 1,005,648 (90.97%) number of supplementary alignments = 3,721 (0.34%) number of secondary alignments = 0 number of mapped bases = 58,254,579 bp number of sequenced bases = 58,234,964 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,584 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5987 >>>>>>> ACTG content number of A's = 14,760,327 bp (25.35%) number of C's = 9,821,279 bp (16.86%) number of T's = 18,843,067 bp (32.36%) number of G's = 14,809,821 bp (25.43%) number of N's = 470 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 295,088 number of insertions = 4,012 mapped reads with insertion percentage = 0.4% number of deletions = 11,612 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.31% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 0.1933X There is a 1.72% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% 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 5898693 0.023665710345411737 0.3285195853536424 chr2 243199373 5175978 0.021282859146187025 0.2322055351425183 chr3 198022430 3625894 0.018310521691911365 0.14620060607454927 chr4 191154276 2648312 0.013854317336850995 0.1439467632444108 chr5 180915260 3602040 0.019910094925104715 0.15092057706348014 chr6 171115067 3792464 0.022163238261187133 0.16783725798085009 chr7 159138663 3536249 0.02222118078244757 0.23256994756523588 chr8 146364022 5180571 0.035395112331635704 0.24396162243823874 chr9 141213431 2113291 0.014965226643349526 0.15741638373778494 chr10 135534747 2572807 0.018982637714297722 0.2144586872594951 chr11 135006516 2921730 0.021641399886209937 0.17966241597507163 chr12 133851895 1824818 0.013633112926791213 0.12906904636900143 chr13 115169878 1419173 0.012322432085931357 0.11892924691114753 chr14 107349540 1096023 0.0102098527855825 0.11140425638650478 chr15 102531392 1496800 0.014598455856329347 0.12984693483417434 chr16 90354753 1755498 0.01942895024017165 0.15570758232816453 chr17 81195210 1319476 0.01625066306251317 0.14038624656659413 chr18 78077248 1536174 0.019675053096133717 0.25106639266826836 chr19 59128983 1220737 0.020645323800005153 0.25672607360180294 chr20 63025520 1098886 0.017435572130146647 0.14401609188516032 chr21 48129895 530484 0.011021923068812015 0.12859858689652512 chr22 51304566 1070375 0.020863152803982397 0.1558767475543757 chrMT 16571 4129 0.2491702371613059 0.4884257353730366 chrX 155270560 2647927 0.017053632060063415 0.1503906835755079 chrY 59373566 166050 0.002796699123647045 0.09790082685301114