BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173931.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 = 14,079,468 number of mapped reads = 13,756,488 (97.71%) number of supplementary alignments = 1,870,108 (13.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,882,417 number of mapped paired reads (second in pair) = 6,874,071 number of mapped paired reads (both in pair) = 13,552,964 number of mapped paired reads (singletons) = 203,524 number of mapped bases = 1,557,064,421 bp number of sequenced bases = 1,555,950,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,036,102 duplication rate = 65.07% >>>>>>> Insert size mean insert size = 1,122,111.581 std insert size = 9,741,989.4059 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.4347 >>>>>>> ACTG content number of A's = 463,227,545 bp (29.77%) number of C's = 310,005,978 bp (19.92%) number of T's = 460,128,184 bp (29.57%) number of G's = 322,576,316 bp (20.73%) number of N's = 12,256 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 13,585,325 number of insertions = 179,392 mapped reads with insertion percentage = 1.25% number of deletions = 469,548 mapped reads with deletion percentage = 3.32% homopolymer indels = 40.94% >>>>>>> Coverage mean coverageData = 0.503X std coverageData = 8.9023X There is a 10.53% of reference with a coverageData >= 1X There is a 8% of reference with a coverageData >= 2X There is a 6.03% of reference with a coverageData >= 3X There is a 4.85% of reference with a coverageData >= 4X There is a 3.66% of reference with a coverageData >= 5X There is a 3.01% of reference with a coverageData >= 6X There is a 2.27% of reference with a coverageData >= 7X There is a 1.94% of reference with a coverageData >= 8X There is a 1.47% of reference with a coverageData >= 9X There is a 1.3% of reference with a coverageData >= 10X There is a 0.98% of reference with a coverageData >= 11X There is a 0.89% of reference with a coverageData >= 12X There is a 0.67% of reference with a coverageData >= 13X There is a 0.61% of reference with a coverageData >= 14X There is a 0.46% of reference with a coverageData >= 15X There is a 0.42% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 125893691 0.5050887756865409 4.212260858281553 chr2 243199373 138159259 0.5680905229965375 29.406136321399952 chr3 198022430 100021943 0.5051041086608219 2.1380904167402734 chr4 191154276 102126266 0.5342609547484044 4.310938814271468 chr5 180915260 90264849 0.4989344127189713 2.1150497444644807 chr6 171115067 85966127 0.5023878288870962 2.8238850341722217 chr7 159138663 95758952 0.6017327919865708 4.512935993951953 chr8 146364022 85326670 0.5829757124329366 5.314213644333646 chr9 141213431 73244340 0.5186782835125647 3.9606644559695576 chr10 135534747 75376893 0.5561444180804794 5.424378886261287 chr11 135006516 72358226 0.5359609902087985 2.4064909322761774 chr12 133851895 69304614 0.5177708840057886 2.345375157333596 chr13 115169878 46647058 0.4050282835239263 1.9240979270493885 chr14 107349540 52749586 0.49138157462062715 2.1842872348260842 chr15 102531392 49780872 0.48551834739549815 2.211919529114158 chr16 90354753 48087357 0.5322061696079231 3.451823321778401 chr17 81195210 41462225 0.510648657722543 2.5950158135860497 chr18 78077248 45319125 0.5804395795302622 5.731906678473852 chr19 59128983 29699250 0.502279060000068 3.297028647764796 chr20 63025520 35984967 0.570958668805906 2.691286986876824 chr21 48129895 22030697 0.45773415878010953 3.327230291574688 chr22 51304566 19413436 0.3783958722114519 2.4887650426529904 chrMT 16571 1558905 94.07428640395872 68.21583197520013 chrX 155270560 38554634 0.24830614380472382 1.542560952718574 chrY 59373566 11974479 0.20168030668732279 3.4190015027151794