BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081917.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 = 2,177,354 number of mapped reads = 2,009,009 (92.27%) number of supplementary alignments = 14,435 (0.66%) number of secondary alignments = 0 number of mapped bases = 137,701,531 bp number of sequenced bases = 137,648,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,814 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2492 >>>>>>> ACTG content number of A's = 39,011,329 bp (28.34%) number of C's = 25,831,916 bp (18.77%) number of T's = 42,876,773 bp (31.15%) number of G's = 29,927,106 bp (21.74%) number of N's = 1,564 bp (0%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,167,818 number of insertions = 11,224 mapped reads with insertion percentage = 0.55% number of deletions = 32,421 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 0.0445X std coverageData = 0.3474X There is a 3.88% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10861753 0.04357763666313995 0.5133046063822626 chr2 243199373 12140088 0.04991825369549781 0.4506454750777892 chr3 198022430 9607270 0.048516069618982055 0.24542267763455283 chr4 191154276 8926409 0.04669740686313499 0.2544070833709963 chr5 180915260 8515253 0.047067632658516476 0.24067853108330609 chr6 171115067 8261294 0.04827917345232959 0.2845903326775508 chr7 159138663 7502854 0.04714664468432791 0.4547196509163407 chr8 146364022 6807702 0.04651212714009731 0.4515735204621205 chr9 141213431 5737163 0.04062760149209886 0.33635863071187116 chr10 135534747 6524984 0.04814251802159634 0.3788766605980214 chr11 135006516 6108718 0.04524757901314926 0.3139573568854343 chr12 133851895 6176762 0.04614624245700817 0.2405844869983025 chr13 115169878 4599241 0.03993440889118594 0.22151858549917675 chr14 107349540 4029119 0.03753270857052578 0.22898339740918083 chr15 102531392 3948270 0.03850791375191707 0.22258971918512976 chr16 90354753 3873530 0.04287024059486943 0.25841949456615015 chr17 81195210 3539313 0.04359016991273253 0.25297754263576533 chr18 78077248 3821856 0.04894967609514106 0.6293796375187192 chr19 59128983 2431569 0.041123132457732275 0.4433005377306798 chr20 63025520 2820942 0.04475872630642318 0.23997433781568694 chr21 48129895 1766839 0.03670980375087043 0.2268112354131315 chr22 51304566 1464826 0.028551571803570076 0.1866128382226559 chrMT 16571 10992 0.6633274998491341 0.8839266138226434 chrX 155270560 7879413 0.05074634238454476 0.27081063501539276 chrY 59373566 345371 0.005816915224529381 0.13847937292035162