BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004072.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,206,891 number of mapped reads = 1,993,233 (90.32%) number of supplementary alignments = 13,498 (0.61%) number of secondary alignments = 0 number of mapped bases = 134,162,198 bp number of sequenced bases = 134,103,746 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,751 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7794 >>>>>>> ACTG content number of A's = 37,311,402 bp (27.82%) number of C's = 24,750,030 bp (18.46%) number of T's = 42,675,967 bp (31.82%) number of G's = 29,356,421 bp (21.89%) number of N's = 9,926 bp (0.01%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,140,469 number of insertions = 9,746 mapped reads with insertion percentage = 0.48% number of deletions = 33,368 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.3994X There is a 3.54% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9809367 0.03935543655074785 0.7811885215899573 chr2 243199373 10572674 0.043473278197966404 0.41420692290397565 chr3 198022430 9521063 0.048080730046591184 0.2587931240790108 chr4 191154276 8614606 0.04506624795565651 0.27284382498786125 chr5 180915260 9532657 0.052691282095274884 0.2732295749260346 chr6 171115067 7641409 0.04465655265763359 0.2766325476295248 chr7 159138663 7284802 0.04577644340269467 0.4901951781266093 chr8 146364022 7512578 0.051328037432587084 0.5129959115825808 chr9 141213431 5790418 0.041004725676554096 0.35285998612453984 chr10 135534747 6462848 0.04768406731891417 0.355697420041096 chr11 135006516 5841276 0.04326662277545182 0.337548776206777 chr12 133851895 5641836 0.0421498403141771 0.24728836743990643 chr13 115169878 4670906 0.04055666360955944 0.24276134139006011 chr14 107349540 4026945 0.03751245697000658 0.25269731557130826 chr15 102531392 3790988 0.03697392501995877 0.22769940599113936 chr16 90354753 3850313 0.04261328676312136 0.2698226320039595 chr17 81195210 3275109 0.040336234120214726 0.25892000723576875 chr18 78077248 3537187 0.04530368437166228 0.7290363671437967 chr19 59128983 2652937 0.044866947906071715 0.49863965735558047 chr20 63025520 2549896 0.04045815092045254 0.24554572149472528 chr21 48129895 1752869 0.03641954755978587 0.24855734578149255 chr22 51304566 1519993 0.029626856213928406 0.20120288643479112 chrMT 16571 3513 0.21199686198781004 0.5246390123240503 chrX 155270560 7945904 0.05117456908766221 0.2933478049350209 chrY 59373566 360104 0.006065055954361912 0.14418236226574394