BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708573.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,373,513 number of mapped reads = 3,591,375 (82.12%) number of supplementary alignments = 94 (0%) number of secondary alignments = 0 number of mapped bases = 179,083,653 bp number of sequenced bases = 179,067,351 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,018 duplication rate = 0.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1612 >>>>>>> ACTG content number of A's = 55,387,019 bp (30.93%) number of C's = 34,136,674 bp (19.06%) number of T's = 55,053,523 bp (30.74%) number of G's = 34,483,602 bp (19.26%) number of N's = 6,533 bp (0%) GC percentage = 38.32% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 283,332 number of insertions = 12,281 mapped reads with insertion percentage = 0.34% number of deletions = 9,594 mapped reads with deletion percentage = 0.27% homopolymer indels = 48% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.2565X There is a 5.29% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.05% 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 15552989 0.062398997994873605 0.2689300124505963 chr2 243199373 14938863 0.06142640425310636 0.2633224759740466 chr3 198022430 16380816 0.08272202295467236 0.30713999934573327 chr4 191154276 12986879 0.06793925446899236 0.2763049176293783 chr5 180915260 14181633 0.07838826310174167 0.2990397338738057 chr6 171115067 8214360 0.04800489018304858 0.23052597942138556 chr7 159138663 11856671 0.0745052822267333 0.2921447706632477 chr8 146364022 7909650 0.054040944570380826 0.24397636157861616 chr9 141213431 6339216 0.044891027398095015 0.2237261269211418 chr10 135534747 11307151 0.08342621541913528 0.3097715633939868 chr11 135006516 5531948 0.0409754148459027 0.21316054976171897 chr12 133851895 7556842 0.056456742730463395 0.2526275966862882 chr13 115169878 5345821 0.04641683305421232 0.22818633590724444 chr14 107349540 6158226 0.05736611447054175 0.25453734116593857 chr15 102531392 3991015 0.03892481046195101 0.21009635706090793 chr16 90354753 4539504 0.050240898782601955 0.23619688024457886 chr17 81195210 2693252 0.033170084787021305 0.1933248010679427 chr18 78077248 6283559 0.08047874586973147 0.30323479572199274 chr19 59128983 1758210 0.02973516388739512 0.17903009191477368 chr20 63025520 5075982 0.08053851836525902 0.3037901555277285 chr21 48129895 1555390 0.03231650515755333 0.1909304259181382 chr22 51304566 1511901 0.029469131460930786 0.1820264845685692 chrMT 16571 300 0.018103916480598635 0.13332728411192565 chrX 155270560 7227838 0.04654995769964377 0.22810314468665235 chrY 59373566 185637 0.0031265934069043453 0.05879060184628617