BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818865.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 = 562,570 number of mapped reads = 554,315 (98.53%) number of supplementary alignments = 8,190 (1.46%) number of secondary alignments = 0 number of mapped bases = 51,314,328 bp number of sequenced bases = 51,282,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,519 duplication rate = 9.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.172 >>>>>>> ACTG content number of A's = 14,807,845 bp (28.87%) number of C's = 11,550,972 bp (22.52%) number of T's = 14,092,646 bp (27.48%) number of G's = 10,830,299 bp (21.12%) number of N's = 882 bp (0%) GC percentage = 43.64% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 310,928 number of insertions = 6,929 mapped reads with insertion percentage = 1.21% number of deletions = 16,461 mapped reads with deletion percentage = 2.9% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.2257X There is a 1.38% of reference with a coverageData >= 1X There is a 0.19% 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 4718456 0.01893056868251494 0.333891042971615 chr2 243199373 3770349 0.015503119738717418 0.3168275941915341 chr3 198022430 3162528 0.01597055444678666 0.1455828722107114 chr4 191154276 2443111 0.012780833634085172 0.15052352118443768 chr5 180915260 2536811 0.014022095206341356 0.13895131988064377 chr6 171115067 2466452 0.014413996635375188 0.14359307074942604 chr7 159138663 4248502 0.026696856187612937 0.4197156154106071 chr8 146364022 5917328 0.04042884254711175 0.2673130110380587 chr9 141213431 1786939 0.012654171684278388 0.17374156691002243 chr10 135534747 2004266 0.014787838870573906 0.2672218864026691 chr11 135006516 2164095 0.01602955963992138 0.1618713824557436 chr12 133851895 1953258 0.014592680962791002 0.13906974436858374 chr13 115169878 1370014 0.01189559304734177 0.1251117886473796 chr14 107349540 1758063 0.01637699611940582 0.15328222664224134 chr15 102531392 1242621 0.012119419972372949 0.1260282021532579 chr16 90354753 1244835 0.013777194432704608 0.2133380008619603 chr17 81195210 1453956 0.01790691840072832 0.17601726170559884 chr18 78077248 892497 0.01143094848834836 0.1947438611678637 chr19 59128983 907446 0.015346890035297918 0.2838958614034044 chr20 63025520 2062573 0.03272599734202907 0.21716132099500307 chr21 48129895 611099 0.012696869585940298 0.13983951366269312 chr22 51304566 498012 0.0097069722800111 0.1183650501695875 chrMT 16571 37445 2.259670508720053 2.139278508284733 chrX 155270560 1879910 0.012107317704012919 0.13798610166149758 chrY 59373566 183762 0.0030950136968360634 0.23295388270539893