BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438258.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 795,555,712 number of mapped reads = 791,315,274 (99.47%) number of supplementary alignments = 21,389,618 (2.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 395,946,177 number of mapped paired reads (second in pair) = 395,369,097 number of mapped paired reads (both in pair) = 788,636,222 number of mapped paired reads (singletons) = 2,679,052 number of mapped bases = 112,077,834,314 bp number of sequenced bases = 112,041,931,311 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 336,327,076 duplication rate = 37.49% >>>>>>> Insert size mean insert size = 107,086.3854 std insert size = 3,155,936.669 median insert size = 456 >>>>>>> Mapping quality mean mapping quality = 54.2554 >>>>>>> ACTG content number of A's = 34,525,586,764 bp (30.81%) number of C's = 21,165,175,052 bp (18.89%) number of T's = 32,522,388,832 bp (29.03%) number of G's = 23,828,574,973 bp (21.27%) number of N's = 205,690 bp (0%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 629,661,965 number of insertions = 14,916,622 mapped reads with insertion percentage = 1.84% number of deletions = 13,203,981 mapped reads with deletion percentage = 1.62% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 36.2044X std coverageData = 109.517X There is a 90.87% of reference with a coverageData >= 1X There is a 90.14% of reference with a coverageData >= 2X There is a 89.37% of reference with a coverageData >= 3X There is a 88.57% of reference with a coverageData >= 4X There is a 87.7% of reference with a coverageData >= 5X There is a 86.77% of reference with a coverageData >= 6X There is a 85.76% of reference with a coverageData >= 7X There is a 84.69% of reference with a coverageData >= 8X There is a 83.55% of reference with a coverageData >= 9X There is a 82.34% of reference with a coverageData >= 10X There is a 81.05% of reference with a coverageData >= 11X There is a 79.71% of reference with a coverageData >= 12X There is a 78.31% of reference with a coverageData >= 13X There is a 76.85% of reference with a coverageData >= 14X There is a 75.34% of reference with a coverageData >= 15X There is a 73.79% of reference with a coverageData >= 16X There is a 72.2% of reference with a coverageData >= 17X There is a 70.58% of reference with a coverageData >= 18X There is a 68.94% of reference with a coverageData >= 19X There is a 67.27% of reference with a coverageData >= 20X There is a 65.59% of reference with a coverageData >= 21X There is a 63.9% of reference with a coverageData >= 22X There is a 62.2% of reference with a coverageData >= 23X There is a 60.51% of reference with a coverageData >= 24X There is a 58.82% of reference with a coverageData >= 25X There is a 57.14% of reference with a coverageData >= 26X There is a 55.47% of reference with a coverageData >= 27X There is a 53.82% of reference with a coverageData >= 28X There is a 52.19% of reference with a coverageData >= 29X There is a 50.58% of reference with a coverageData >= 30X There is a 48.99% of reference with a coverageData >= 31X There is a 47.43% of reference with a coverageData >= 32X There is a 45.9% of reference with a coverageData >= 33X There is a 44.4% of reference with a coverageData >= 34X There is a 42.93% of reference with a coverageData >= 35X There is a 41.5% of reference with a coverageData >= 36X There is a 40.1% of reference with a coverageData >= 37X There is a 38.73% of reference with a coverageData >= 38X There is a 37.4% of reference with a coverageData >= 39X There is a 36.1% of reference with a coverageData >= 40X There is a 34.84% of reference with a coverageData >= 41X There is a 33.61% of reference with a coverageData >= 42X There is a 32.42% of reference with a coverageData >= 43X There is a 31.27% of reference with a coverageData >= 44X There is a 30.14% of reference with a coverageData >= 45X There is a 29.06% of reference with a coverageData >= 46X There is a 28% of reference with a coverageData >= 47X There is a 26.99% of reference with a coverageData >= 48X There is a 26% of reference with a coverageData >= 49X There is a 25.05% of reference with a coverageData >= 50X There is a 24.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8768719346 35.180330989024895 45.50587126860422 chr2 243199373 9614548624 39.53360777784571 198.54185628538627 chr3 198022430 7867800981 39.73186765256845 29.40245711551242 chr4 191154276 7787688814 40.74033276660785 38.65690901946064 chr5 180915260 7241461865 40.026816228769206 29.834137209446528 chr6 171115067 6835543124 39.94705576686593 40.11539082887462 chr7 159138663 5994378888 37.66764640972257 32.25981620859548 chr8 146364022 5794037798 39.586489349138 34.167882392484145 chr9 141213431 4785897174 33.89123215907133 56.864225027210516 chr10 135534747 5068879271 37.39911264968828 82.61429302730166 chr11 135006516 5065814488 37.52274066534685 32.73956425466658 chr12 133851895 5039779116 37.65190710224909 31.121813025159813 chr13 115169878 3854136655 33.46479758361817 30.063420690616294 chr14 107349540 3392746646 31.60466869257195 31.015143962450207 chr15 102531392 3081340801 30.0526574436832 30.117077250917593 chr16 90354753 2900242663 32.09839622936051 91.25723760767752 chr17 81195210 2484429459 30.598226902793897 52.35482301696667 chr18 78077248 3068771028 39.304292948439986 69.12129542742694 chr19 59128983 1440595196 24.363605171426677 32.5747865217839 chr20 63025520 2142254721 33.99027443169053 34.38238021111966 chr21 48129895 1482612459 30.804398368207536 48.626060067828185 chr22 51304566 968794479 18.883201916180326 26.373876473920227 chrMT 16571 564258015 34050.933256894576 12626.741414715423 chrX 155270560 6685307396 43.05585937218234 33.38013254201412 chrY 59373566 147795307 2.4892442370734478 39.55581334837291