BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524480.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 = 1,297,172 number of mapped reads = 1,183,486 (91.24%) number of supplementary alignments = 2,642 (0.2%) number of secondary alignments = 0 number of mapped bases = 68,195,977 bp number of sequenced bases = 68,174,576 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,773 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0899 >>>>>>> ACTG content number of A's = 17,212,906 bp (25.25%) number of C's = 12,455,421 bp (18.27%) number of T's = 22,085,313 bp (32.4%) number of G's = 16,419,517 bp (24.08%) number of N's = 1,419 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 324,676 number of insertions = 4,806 mapped reads with insertion percentage = 0.4% number of deletions = 12,526 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 0.2195X There is a 1.98% of reference with a coverageData >= 1X There is a 0.16% 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 6671818 0.026767508033610877 0.37650545835223775 chr2 243199373 5380017 0.02212183746049378 0.25044851069143903 chr3 198022430 3755162 0.018963316428346023 0.15120587482419948 chr4 191154276 3832140 0.02004736739449135 0.17103749824200482 chr5 180915260 3711150 0.020513194962105463 0.15675673352762678 chr6 171115067 2993566 0.0174944617822579 0.1777003662857565 chr7 159138663 3388690 0.02129394539402408 0.27747620115018906 chr8 146364022 6253474 0.042725486185396025 0.2525350413116628 chr9 141213431 2947313 0.020871336239964313 0.19750160952520998 chr10 135534747 3574549 0.026373672280511212 0.21969539043652245 chr11 135006516 2308624 0.017100093154022285 0.21679237105703647 chr12 133851895 3123417 0.023334873219389235 0.16715680167800978 chr13 115169878 1549556 0.013454524975705887 0.12870260376346002 chr14 107349540 1658564 0.015450126754152835 0.13811237646574157 chr15 102531392 1840143 0.017947118088477723 0.15453904636486912 chr16 90354753 2110633 0.02335940202282441 0.1759860855177541 chr17 81195210 2379852 0.029310251183536567 0.19271298945584406 chr18 78077248 1611328 0.02063761263716672 0.30698299899221093 chr19 59128983 1401219 0.023697667859431983 0.27600851572022134 chr20 63025520 1908955 0.030288603727505938 0.19344149328483448 chr21 48129895 931416 0.019352130313186847 0.1591906700344046 chr22 51304566 559422 0.010903941766118828 0.11330880099949404 chrMT 16571 4727 0.28525737734596585 0.5540993540768129 chrX 155270560 4090361 0.026343442053664262 0.19261591248327245 chrY 59373566 209881 0.0035349232687152394 0.10036812370891181