BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717011.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,043,703 number of mapped reads = 1,914,154 (93.66%) number of supplementary alignments = 32,063 (1.57%) number of secondary alignments = 0 number of mapped bases = 151,737,643 bp number of sequenced bases = 151,671,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,664 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2447 >>>>>>> ACTG content number of A's = 36,270,125 bp (23.91%) number of C's = 30,088,865 bp (19.84%) number of T's = 46,410,614 bp (30.6%) number of G's = 38,893,032 bp (25.64%) number of N's = 9,008 bp (0.01%) GC percentage = 45.48% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,193,875 number of insertions = 14,265 mapped reads with insertion percentage = 0.73% number of deletions = 37,161 mapped reads with deletion percentage = 1.91% homopolymer indels = 43.31% >>>>>>> Coverage mean coverageData = 0.049X std coverageData = 0.5154X There is a 4.12% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14246411 0.05715697294090192 0.7918272407532848 chr2 243199373 11364190 0.046727875404514306 0.8728345162622092 chr3 198022430 10894921 0.05501862087037312 0.2751230966072234 chr4 191154276 6078227 0.03179749429199272 0.25420248748710755 chr5 180915260 8527806 0.04713701873462747 0.2501697261362253 chr6 171115067 9915685 0.05794746876381143 0.33031538902057833 chr7 159138663 8921040 0.0560582817011602 0.7936415187451398 chr8 146364022 10611266 0.07249914189977644 0.6996894248246113 chr9 141213431 7990299 0.05658313761953705 0.503107093796236 chr10 135534747 8102592 0.059782396613025 0.5322311991937766 chr11 135006516 6187818 0.04583347665974878 0.40700783749076963 chr12 133851895 6861345 0.051260723652810446 0.26650125673332914 chr13 115169878 4489548 0.03898196366935459 0.22434915525936888 chr14 107349540 4019958 0.03744737052436368 0.26268668087005226 chr15 102531392 2894727 0.028232592414233485 0.1989313166746739 chr16 90354753 4082559 0.04518366620956841 0.28126238113073454 chr17 81195210 5013603 0.0617475218057814 0.3412211108775045 chr18 78077248 3631628 0.046513268500447146 0.8372300468888308 chr19 59128983 3149883 0.053271388077146535 0.6669589389865697 chr20 63025520 2772152 0.04398459544641599 0.26836810803751615 chr21 48129895 2523310 0.052427083001116044 0.2891187793083967 chr22 51304566 2490379 0.04854107917022434 0.2629102709850325 chrMT 16571 29275 1.7666405165650836 2.230194912275073 chrX 155270560 6514807 0.04195777357922841 0.30258128302432447 chrY 59373566 424214 0.007144829401016607 0.2526049812872325