BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053677.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,600,071 number of mapped reads = 6,318,289 (83.13%) number of supplementary alignments = 180 (0%) number of secondary alignments = 0 number of mapped bases = 298,636,321 bp number of sequenced bases = 298,571,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,235,231 duplication rate = 15.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9047 >>>>>>> ACTG content number of A's = 88,198,821 bp (29.54%) number of C's = 57,594,825 bp (19.29%) number of T's = 89,487,528 bp (29.97%) number of G's = 63,062,063 bp (21.12%) number of N's = 228,747 bp (0.08%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,793,985 number of insertions = 12,489 mapped reads with insertion percentage = 0.2% number of deletions = 42,683 mapped reads with deletion percentage = 0.67% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 0.0965X std coverageData = 0.6893X There is a 4.79% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 23572731 0.09457441231410212 0.7550136976496511 chr2 243199373 27476094 0.11297765146787611 0.7931823899470865 chr3 198022430 20083086 0.10141823832785003 0.6569948846356066 chr4 191154276 14398560 0.07532428937137665 0.564140273864073 chr5 180915260 17343407 0.095864809856283 0.6393519276819846 chr6 171115067 18917680 0.11055531422022585 0.7681182450451359 chr7 159138663 15596369 0.09800490154928598 0.7230312456585158 chr8 146364022 17258894 0.11791759862953206 0.7675185087479097 chr9 141213431 15854542 0.11227361227417525 0.731048439387393 chr10 135534747 10428226 0.0769413470038056 0.6443224554295961 chr11 135006516 14536871 0.10767532879672267 0.7144715505707048 chr12 133851895 16699344 0.12475986238371896 0.7527878913930888 chr13 115169878 7279694 0.06320831563266915 0.5079346523632376 chr14 107349540 5845638 0.05445424358595295 0.5307633551588834 chr15 102531392 7158076 0.06981350648199529 0.5248368147179683 chr16 90354753 7463534 0.08260256104070142 0.612643400311601 chr17 81195210 6965674 0.08578922328053588 0.6037250742392571 chr18 78077248 11089074 0.14202695771244397 0.8633338487380213 chr19 59128983 6023671 0.10187340783453015 0.7288182601712665 chr20 63025520 6567006 0.10419598283362042 0.6885243813678198 chr21 48129895 2930656 0.06089055461267888 0.5458764203353796 chr22 51304566 4190953 0.08168771956866373 0.6065228624875406 chrMT 16571 21548 1.3003439744131313 2.3846990366377345 chrX 155270560 20282263 0.1306252969010996 0.8009467701166326 chrY 59373566 652730 0.010993612881530477 0.2137034451021666