BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708579.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 = 5,065,414 number of mapped reads = 4,956,296 (97.85%) number of supplementary alignments = 166 (0%) number of secondary alignments = 0 number of mapped bases = 247,187,829 bp number of sequenced bases = 247,166,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,703 duplication rate = 1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7777 >>>>>>> ACTG content number of A's = 76,588,611 bp (30.99%) number of C's = 46,821,921 bp (18.94%) number of T's = 76,285,556 bp (30.86%) number of G's = 47,461,448 bp (19.2%) number of N's = 8,940 bp (0%) GC percentage = 38.15% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 360,397 number of insertions = 15,351 mapped reads with insertion percentage = 0.31% number of deletions = 12,595 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.41% >>>>>>> Coverage mean coverageData = 0.0798X std coverageData = 0.295X There is a 7.37% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0% 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 18644607 0.07480265014063897 0.28735207239428634 chr2 243199373 21533605 0.08854301199205805 0.30898505604665505 chr3 198022430 19394864 0.09794276335261616 0.32548369182879316 chr4 191154276 18444285 0.09648900032976505 0.32169907002283005 chr5 180915260 17385889 0.0960996269745294 0.32190642686772003 chr6 171115067 16245434 0.09493865318125376 0.3201934985721144 chr7 159138663 13151405 0.08264116809879193 0.29990374868707287 chr8 146364022 13927710 0.09515801636005876 0.3209980335975751 chr9 141213431 10437259 0.07391123440659125 0.28440732661449586 chr10 135534747 10426081 0.0769255208039013 0.28800296791805935 chr11 135006516 11408105 0.08450040292870012 0.3037805199934885 chr12 133851895 11229645 0.08389604794164475 0.3020027307348384 chr13 115169878 9625301 0.0835748128516729 0.3018549796020978 chr14 107349540 7948022 0.07403871502383709 0.28556073629575046 chr15 102531392 6514552 0.06353714577482768 0.2644263895309899 chr16 90354753 4479814 0.04958028051938784 0.23184941693387673 chr17 81195210 4045998 0.049830501084977795 0.2327317955700743 chr18 78077248 7020315 0.08991499034392196 0.31132402627336814 chr19 59128983 2066024 0.03494096964258628 0.19333475105694897 chr20 63025520 3973396 0.06304423985712454 0.26253034915472595 chr21 48129895 3078564 0.06396365502147885 0.2662397790411567 chr22 51304566 1456487 0.02838903266426618 0.17539729750631317 chrMT 16571 200 0.012069277653732424 0.10919528465391506 chrX 155270560 14414968 0.09283774077970737 0.3172957960279159 chrY 59373566 335299 0.005647277443298589 0.07923043299548826