BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004138.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 = 1,687,240 number of mapped reads = 1,373,528 (81.41%) number of supplementary alignments = 17,342 (1.03%) number of secondary alignments = 0 number of mapped bases = 89,198,175 bp number of sequenced bases = 89,160,412 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,068 duplication rate = 4.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2724 >>>>>>> ACTG content number of A's = 24,733,807 bp (27.74%) number of C's = 16,263,012 bp (18.24%) number of T's = 28,430,260 bp (31.89%) number of G's = 19,718,763 bp (22.12%) number of N's = 14,570 bp (0.02%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 821,134 number of insertions = 6,644 mapped reads with insertion percentage = 0.48% number of deletions = 22,539 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.2948X There is a 2.33% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 6450508 0.025879606534661353 0.5511160215169325 chr2 243199373 6512458 0.026778268050880214 0.2748578005425078 chr3 198022430 5759226 0.029083705315604905 0.20233024512025458 chr4 191154276 4833302 0.025284822820285748 0.2028283839882209 chr5 180915260 6344800 0.03507056287015258 0.22453892161368483 chr6 171115067 4835937 0.02826131611192368 0.20943266780168684 chr7 159138663 3691376 0.023195972181819825 0.2862074907914943 chr8 146364022 6495481 0.04437894580404466 0.37979853447876377 chr9 141213431 2720475 0.019264987620051525 0.26339888981198895 chr10 135534747 3944551 0.029103614293093417 0.27672370597684254 chr11 135006516 3550675 0.026300026881665474 0.2857603845325852 chr12 133851895 3608060 0.02695561388951572 0.19841563723079067 chr13 115169878 3831099 0.033264765636028544 0.21680938055689528 chr14 107349540 3394378 0.031619865348281886 0.22169366194223275 chr15 102531392 2814557 0.027450685542238614 0.19618523248893177 chr16 90354753 2760477 0.03055154165492545 0.23016869218948544 chr17 81195210 2114151 0.026037878342823426 0.21689610835787804 chr18 78077248 2275061 0.029138591052799402 0.48873611621403706 chr19 59128983 1330234 0.022497156766589407 0.3882181064033904 chr20 63025520 2399564 0.03807289491621806 0.24324379115696287 chr21 48129895 1094447 0.022739442917961903 0.19241734361251217 chr22 51304566 1100815 0.021456472314764344 0.173470779484632 chrMT 16571 126479 7.632550841832116 5.250436187585317 chrX 155270560 6902446 0.04445431252389378 0.2705423023589846 chrY 59373566 307618 0.005181059867618529 0.13001337021180975