BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080777.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,861,337 number of mapped reads = 2,510,213 (87.73%) number of supplementary alignments = 26,317 (0.92%) number of secondary alignments = 0 number of mapped bases = 166,348,642 bp number of sequenced bases = 166,291,254 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,706 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9342 >>>>>>> ACTG content number of A's = 47,554,730 bp (28.6%) number of C's = 32,276,845 bp (19.41%) number of T's = 50,530,811 bp (30.39%) number of G's = 35,925,447 bp (21.6%) number of N's = 3,421 bp (0%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,249,338 number of insertions = 12,509 mapped reads with insertion percentage = 0.49% number of deletions = 35,768 mapped reads with deletion percentage = 1.41% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.3859X There is a 4.56% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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% 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 21600495 0.08666174998215952 0.6962754158904795 chr2 243199373 12640104 0.05197424583820782 0.42423089761292454 chr3 198022430 10580421 0.053430416948221475 0.2632098748083891 chr4 191154276 9555827 0.049990129438694846 0.263152378746691 chr5 180915260 11837635 0.06543193205481948 0.2902885979236823 chr6 171115067 11504667 0.06723351252289197 0.4107687055839542 chr7 159138663 11803817 0.07417315677711833 0.5207556759798363 chr8 146364022 7131083 0.04872155672245738 0.48054652100851647 chr9 141213431 5563120 0.03939511957612587 0.3071386745839125 chr10 135534747 6531381 0.048189716250401825 0.37076047554041874 chr11 135006516 6811414 0.05045248334532238 0.2943282560830113 chr12 133851895 5799448 0.04332735072596469 0.23887125988305405 chr13 115169878 7193254 0.06245777216157162 0.2851957641399604 chr14 107349540 3796941 0.035369886074965946 0.2361327626293716 chr15 102531392 3786011 0.036925383788800996 0.22550092728565038 chr16 90354753 4334042 0.04796695089189165 0.26778454229864623 chr17 81195210 3705205 0.04563329536311317 0.25019154921108155 chr18 78077248 2040578 0.02613537300904868 0.5496782079065526 chr19 59128983 2707453 0.045788932307528445 0.4965492320239051 chr20 63025520 2867831 0.045502694781415526 0.25308691785889825 chr21 48129895 2693632 0.055965881496313256 0.2798717088629434 chr22 51304566 805404 0.015698485783896897 0.1388283550976323 chrMT 16571 31657 1.9103856134210369 1.7515396899592803 chrX 155270560 10630642 0.0684652776418144 0.3197077877265483 chrY 59373566 396580 0.00667940342340226 0.13646734698136614