BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818816.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,572,186 number of mapped reads = 1,530,630 (97.36%) number of supplementary alignments = 10,024 (0.64%) number of secondary alignments = 0 number of mapped bases = 104,057,157 bp number of sequenced bases = 104,014,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 574,285 duplication rate = 31.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6505 >>>>>>> ACTG content number of A's = 30,543,012 bp (29.36%) number of C's = 22,064,655 bp (21.21%) number of T's = 28,431,403 bp (27.33%) number of G's = 22,969,415 bp (22.08%) number of N's = 6,099 bp (0.01%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 523,432 number of insertions = 12,097 mapped reads with insertion percentage = 0.78% number of deletions = 25,441 mapped reads with deletion percentage = 1.64% homopolymer indels = 40.55% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.4435X There is a 1.81% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 8754156 0.035121902464588045 0.6820633217118091 chr2 243199373 9055349 0.03723426129063252 0.7208740918701951 chr3 198022430 6939799 0.0350455198433834 0.3117550332392256 chr4 191154276 6559116 0.03431320573754782 0.3584979448447709 chr5 180915260 6308266 0.03486862302273451 0.3269569298587466 chr6 171115067 6128381 0.03581438564962839 0.35365810206156434 chr7 159138663 5642071 0.03545380420847195 0.39585818469471823 chr8 146364022 5253064 0.03589040481546756 0.3543633310814667 chr9 141213431 4434094 0.03139994523608735 0.35086946301691063 chr10 135534747 5111084 0.03771050681195428 0.4905458195419206 chr11 135006516 4925156 0.036480876226744494 0.36301685992207694 chr12 133851895 4859579 0.03630564214275786 0.33379939945361553 chr13 115169878 3062660 0.026592543581577813 0.2700868264367361 chr14 107349540 3241748 0.030198061398306875 0.32690255322184564 chr15 102531392 3120969 0.030439155649032833 0.299202461573496 chr16 90354753 3241060 0.03587038747148144 0.4806719043055186 chr17 81195210 3102844 0.03821461881803126 0.35131568029386645 chr18 78077248 2685246 0.034392170174850425 0.44120442478398636 chr19 59128983 2278177 0.03852893935280436 0.5440536451226348 chr20 63025520 2375065 0.03768417936099536 0.3456438743016331 chr21 48129895 1370229 0.028469395164896993 0.3051795941711571 chr22 51304566 1458454 0.02842737233173359 0.30787676803327785 chrMT 16571 104732 6.320197936153521 6.239700914874709 chrX 155270560 3068424 0.019761788712554396 0.27119739331555964 chrY 59373566 977434 0.01646244390980323 0.7532523881100307