BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124970.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,132,650 number of mapped reads = 6,036,456 (98.43%) number of supplementary alignments = 60,019 (0.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,025,500 number of mapped paired reads (second in pair) = 3,010,956 number of mapped paired reads (both in pair) = 6,003,850 number of mapped paired reads (singletons) = 32,606 number of mapped bases = 513,553,529 bp number of sequenced bases = 513,250,242 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 754,744 duplication rate = 8.43% >>>>>>> Insert size mean insert size = 89,855.3833 std insert size = 2,796,692.9914 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 52.1741 >>>>>>> ACTG content number of A's = 147,870,177 bp (28.81%) number of C's = 93,951,381 bp (18.31%) number of T's = 156,022,497 bp (30.4%) number of G's = 115,400,854 bp (22.48%) number of N's = 5,333 bp (0%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 4,021,679 number of insertions = 81,039 mapped reads with insertion percentage = 1.3% number of deletions = 163,040 mapped reads with deletion percentage = 2.64% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.1659X std coverageData = 2.3298X There is a 10.61% of reference with a coverageData >= 1X There is a 3.27% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 42046661 0.168692301873944 1.930372792656254 chr2 243199373 44017869 0.1809949937658762 2.43450577876008 chr3 198022430 37860106 0.19119099790867125 0.6704422836766027 chr4 191154276 30300493 0.15851328902524786 1.7639108600738675 chr5 180915260 30161870 0.16671821934755532 0.589443726456641 chr6 171115067 29020775 0.169598010910401 1.0043680890460522 chr7 159138663 33666726 0.21155591837541077 1.998955620646639 chr8 146364022 33261110 0.22724922112348075 0.959315672282264 chr9 141213431 20124510 0.14251130262531472 2.1578074145218578 chr10 135534747 27064593 0.19968748678152623 7.866382747383975 chr11 135006516 19670982 0.145703945134026 1.0648438945636611 chr12 133851895 23835457 0.17807336235321883 0.5879688924726972 chr13 115169878 14304492 0.12420341367384274 0.47225783388315007 chr14 107349540 16555655 0.1542219463632541 0.6491117552893886 chr15 102531392 13751916 0.13412395688532153 0.5325708036338369 chr16 90354753 18529835 0.20507869685615765 4.133656867275457 chr17 81195210 10174412 0.12530803233343446 1.7696922142458449 chr18 78077248 9855253 0.12622438997849925 2.3780552136265025 chr19 59128983 6807259 0.1151255890871656 1.2077708433338723 chr20 63025520 9889956 0.1569198635727242 0.7145377301024908 chr21 48129895 5535055 0.11500243247985478 0.9994422530516386 chr22 51304566 3812664 0.07431432126333551 0.45241122470151185 chrMT 16571 135558 8.180435700923299 5.70544007929225 chrX 155270560 23406726 0.15074799755987225 0.7971927296210836 chrY 59373566 9763596 0.16444348314871302 3.850357935235472