BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818848.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 = 1,541,904 number of mapped reads = 1,522,117 (98.72%) number of supplementary alignments = 26,094 (1.69%) number of secondary alignments = 0 number of mapped bases = 140,824,861 bp number of sequenced bases = 140,731,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 325,513 duplication rate = 18.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7941 >>>>>>> ACTG content number of A's = 40,721,515 bp (28.94%) number of C's = 29,852,591 bp (21.21%) number of T's = 38,823,202 bp (27.59%) number of G's = 31,331,925 bp (22.26%) number of N's = 1,915 bp (0%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 860,818 number of insertions = 23,405 mapped reads with insertion percentage = 1.49% number of deletions = 47,478 mapped reads with deletion percentage = 3.04% homopolymer indels = 38.64% >>>>>>> Coverage mean coverageData = 0.0455X std coverageData = 0.5677X There is a 3.18% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 10909653 0.043769812713927 0.6886480517961443 chr2 243199373 10596763 0.043572328617804454 0.885189184197111 chr3 198022430 9746697 0.049220166624558644 0.2916113634493297 chr4 191154276 6830189 0.035731290677483984 0.3458664428735979 chr5 180915260 3742514 0.020686557894563456 0.21678905953953845 chr6 171115067 2753143 0.016089424784551557 0.19913524731310792 chr7 159138663 16842998 0.10583850387130625 1.3007365126484218 chr8 146364022 14529360 0.09926865770332548 0.5173455180725461 chr9 141213431 5575406 0.03948212263180547 0.42401049502941834 chr10 135534747 10523147 0.07764169139593406 0.7827188308605844 chr11 135006516 4032629 0.029869884206181575 0.2731784758961693 chr12 133851895 3546745 0.026497532963578888 0.21497251875069465 chr13 115169878 3319084 0.028819028531053927 0.2231274447820037 chr14 107349540 4346661 0.04049072776650929 0.2878406826357727 chr15 102531392 5833485 0.0568946240386554 0.31479953905629887 chr16 90354753 3617126 0.04003249281197194 0.639024349289053 chr17 81195210 4451755 0.05482780326573452 0.3802156183203197 chr18 78077248 1487933 0.019057190642784952 0.43451375195833564 chr19 59128983 2535388 0.04287893806663307 0.6955566369554201 chr20 63025520 6294676 0.09987503474782913 0.4519263734524694 chr21 48129895 1542744 0.032053757856733325 0.2980199363138426 chr22 51304566 1173682 0.022876755258001792 0.2212819838948028 chrMT 16571 324833 19.602498340474323 12.86878957233386 chrX 155270560 5662759 0.03647026841405093 0.28943591115983935 chrY 59373566 605491 0.010197989455442175 0.8234850817348472