BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081038.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 = 2,064,609 number of mapped reads = 1,567,670 (75.93%) number of supplementary alignments = 7,742 (0.37%) number of secondary alignments = 0 number of mapped bases = 98,747,712 bp number of sequenced bases = 98,715,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,862 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2158 >>>>>>> ACTG content number of A's = 28,623,770 bp (29%) number of C's = 18,759,936 bp (19%) number of T's = 29,630,759 bp (30.02%) number of G's = 21,699,440 bp (21.98%) number of N's = 1,256 bp (0%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 766,624 number of insertions = 6,572 mapped reads with insertion percentage = 0.41% number of deletions = 19,206 mapped reads with deletion percentage = 1.21% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.2551X There is a 2.82% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 6679292 0.026797493916775435 0.3164097223957563 chr2 243199373 9191649 0.0377947068144785 0.30420301041326336 chr3 198022430 6992094 0.035309606088562796 0.20727252328252438 chr4 191154276 6590663 0.0344782399740825 0.21079042238160678 chr5 180915260 6205504 0.034300611236442964 0.20467667870822165 chr6 171115067 5832123 0.034083047754058966 0.27868652388117426 chr7 159138663 4663027 0.029301660024628962 0.2725473474942986 chr8 146364022 3960448 0.02705889019638993 0.26016257227369666 chr9 141213431 4267472 0.03022001497860356 0.25897222842255974 chr10 135534747 4219529 0.03113245196082448 0.2321019542655248 chr11 135006516 5002179 0.037051389430714586 0.2857560457404413 chr12 133851895 4625322 0.03455552123486933 0.20750972997106876 chr13 115169878 3892776 0.033800296289278 0.2025644622890729 chr14 107349540 3126672 0.029126086613878364 0.20077960094304287 chr15 102531392 3522483 0.03435516607440578 0.21226744092370686 chr16 90354753 2842410 0.031458334018134054 0.21570241921131733 chr17 81195210 2272877 0.027992747355416656 0.20145732912915515 chr18 78077248 3141977 0.040241902480989085 0.5105578729768186 chr19 59128983 1558843 0.026363433309854155 0.278585120345554 chr20 63025520 1811909 0.02874881476582819 0.1908303671033883 chr21 48129895 1496442 0.031091736227556697 0.2074655137791659 chr22 51304566 1080464 0.021059801967723498 0.15905168671858658 chrMT 16571 15052 0.9083338362199023 1.0613147595894392 chrX 155270560 5512458 0.03550227422378074 0.23177698787346795 chrY 59373566 244047 0.004110364534951463 0.09799522842936985