BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124904.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,696,056 number of mapped reads = 4,596,948 (97.89%) number of supplementary alignments = 18,011 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,302,202 number of mapped paired reads (second in pair) = 2,294,746 number of mapped paired reads (both in pair) = 4,581,484 number of mapped paired reads (singletons) = 15,464 number of mapped bases = 398,390,221 bp number of sequenced bases = 398,167,938 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 399,751 duplication rate = 6.55% >>>>>>> Insert size mean insert size = 28,598.846 std insert size = 1,573,007.324 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.8754 >>>>>>> ACTG content number of A's = 111,558,789 bp (28.02%) number of C's = 74,659,139 bp (18.75%) number of T's = 117,503,147 bp (29.51%) number of G's = 94,441,973 bp (23.72%) number of N's = 4,890 bp (0%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 2,835,080 number of insertions = 53,174 mapped reads with insertion percentage = 1.12% number of deletions = 131,042 mapped reads with deletion percentage = 2.79% homopolymer indels = 47.24% >>>>>>> Coverage mean coverageData = 0.1287X std coverageData = 1.0027X There is a 8.65% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 27048779 0.10852040765828222 1.027537662367016 chr2 243199373 34761259 0.14293317688775456 1.2988623412055238 chr3 198022430 25909856 0.1308430363166435 0.4778882898056773 chr4 191154276 20566540 0.10759131540431771 0.940636320839593 chr5 180915260 23071474 0.12752641208928422 0.4831690498648562 chr6 171115067 21600417 0.1262332848807522 0.6374044693485597 chr7 159138663 24547796 0.15425412993447105 1.5977111136903142 chr8 146364022 21315458 0.14563318026338468 0.7732833955317324 chr9 141213431 19123056 0.13541952677291724 1.149173394695936 chr10 135534747 18987061 0.14008998740374673 1.89572492364772 chr11 135006516 23411070 0.17340696355722562 0.9359175503137047 chr12 133851895 22948682 0.17144831606605196 0.5609557022167277 chr13 115169878 7420803 0.0644335405130845 0.32688639074712467 chr14 107349540 11577178 0.10784562281310195 0.48560888362508764 chr15 102531392 11002351 0.10730714550330107 0.4361008345316164 chr16 90354753 10993071 0.12166566378638653 1.4318659956308895 chr17 81195210 14291089 0.1760090158027795 1.6709607187448425 chr18 78077248 10410458 0.13333536038565294 1.2373081496356255 chr19 59128983 6219156 0.10517948532955489 0.6656423008637006 chr20 63025520 6455618 0.1024286352575909 0.4711868251295146 chr21 48129895 4935252 0.1025402610996762 0.5374176406890971 chr22 51304566 4349726 0.08478243437435959 0.40823689277477465 chrMT 16571 49886 3.0104399251704788 2.7575554043247665 chrX 155270560 26423005 0.17017395313058703 0.6806478654366391 chrY 59373566 971180 0.016357110839527476 0.9927258934435759