BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173918.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,974,178 number of mapped reads = 2,890,433 (97.18%) number of supplementary alignments = 293,463 (9.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,447,757 number of mapped paired reads (second in pair) = 1,442,676 number of mapped paired reads (both in pair) = 2,833,782 number of mapped paired reads (singletons) = 56,651 number of mapped bases = 340,640,351 bp number of sequenced bases = 340,447,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,248,695 duplication rate = 64.51% >>>>>>> Insert size mean insert size = 1,000,094.2251 std insert size = 9,393,828.3218 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.7606 >>>>>>> ACTG content number of A's = 102,165,081 bp (30.01%) number of C's = 66,940,932 bp (19.66%) number of T's = 101,988,563 bp (29.96%) number of G's = 69,348,210 bp (20.37%) number of N's = 4,436 bp (0%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 3,579,565 number of insertions = 35,710 mapped reads with insertion percentage = 1.19% number of deletions = 79,321 mapped reads with deletion percentage = 2.68% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.11X std coverageData = 1.7633X There is a 2.31% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 1.41% of reference with a coverageData >= 3X There is a 1.16% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 29246840 0.11733908578707213 1.3062891112495965 chr2 243199373 35290540 0.14510950239990955 4.899607512908498 chr3 198022430 26128803 0.13194870399277495 1.0578960536164304 chr4 191154276 20914088 0.10940946986715588 1.0583235940047753 chr5 180915260 23115733 0.12777105148565135 1.0348381456410105 chr6 171115067 19052523 0.11134333950849576 0.9950263992409929 chr7 159138663 23432968 0.14724874243790775 1.6304143652567498 chr8 146364022 14759911 0.10084384672074671 1.0330160050510775 chr9 141213431 11884336 0.0841586803453561 0.9278555954025397 chr10 135534747 14440257 0.10654284100297912 1.9628815296782371 chr11 135006516 16168840 0.11976340460485625 1.0195361228839444 chr12 133851895 13266632 0.09911426356720612 0.9132399700595734 chr13 115169878 9374823 0.08139995598501892 0.8309703064175701 chr14 107349540 8146663 0.07588912816952918 0.7921903043436452 chr15 102531392 11307319 0.11028153211847548 0.9447753450322063 chr16 90354753 14407595 0.1594558617187521 1.4464962137410584 chr17 81195210 8312706 0.10237926596901467 0.967098038605048 chr18 78077248 5640912 0.07224783332527294 1.2778316053062853 chr19 59128983 6215422 0.10511633524966936 1.4597567822924464 chr20 63025520 10180363 0.16152763198145767 1.1478939802415404 chr21 48129895 3585819 0.07450294666132141 0.7997515437554547 chr22 51304566 3034026 0.05913754343034497 0.6509483407660398 chrMT 16571 946839 57.138313921911774 47.63894225415531 chrX 155270560 11291002 0.07271824098528401 0.772130249971529 chrY 59373566 495391 0.008343628880232662 0.3814536643481985