BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054576.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 = 9,086,802 number of mapped reads = 6,460,828 (71.1%) number of supplementary alignments = 189 (0%) number of secondary alignments = 0 number of mapped bases = 305,212,850 bp number of sequenced bases = 305,149,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,511,984 duplication rate = 18.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6032 >>>>>>> ACTG content number of A's = 88,838,211 bp (29.11%) number of C's = 59,564,646 bp (19.52%) number of T's = 90,700,255 bp (29.72%) number of G's = 65,940,786 bp (21.61%) number of N's = 105,905 bp (0.03%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,793,263 number of insertions = 12,757 mapped reads with insertion percentage = 0.2% number of deletions = 42,105 mapped reads with deletion percentage = 0.65% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 0.0986X std coverageData = 0.7404X There is a 4.61% of reference with a coverageData >= 1X There is a 1.97% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% 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 0.01% 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 25884432 0.10384901709031248 0.7938674785822343 chr2 243199373 31589213 0.12989019095867488 1.049783273241957 chr3 198022430 19668975 0.09932700553164608 0.6825326295176709 chr4 191154276 14635469 0.07656364956230433 0.5848138267974461 chr5 180915260 15365128 0.08492997218697859 0.6036302351281747 chr6 171115067 18428099 0.10769419270367349 0.7505834754942309 chr7 159138663 15955949 0.10026444045216089 0.8689899791165159 chr8 146364022 16270196 0.11116253692454557 0.7587088341508774 chr9 141213431 16474760 0.11666567325313412 0.7736966235967171 chr10 135534747 10571190 0.0779961613828814 0.6515608996634817 chr11 135006516 14671065 0.10866931045017116 0.7460097703839967 chr12 133851895 16317732 0.12190886053574362 0.7632119659908849 chr13 115169878 7499176 0.06511403962761861 0.5288837110963295 chr14 107349540 6004214 0.055931436688037975 0.5980973835439705 chr15 102531392 8999059 0.08776881718332664 0.6147682835448743 chr16 90354753 7688115 0.08508810820389272 0.6276413271212985 chr17 81195210 8520846 0.10494271768002078 0.707987977099033 chr18 78077248 9537872 0.12215942857002338 0.8595435142473792 chr19 59128983 6470176 0.10942478073739235 0.7949651981551166 chr20 63025520 6793688 0.10779265288092824 0.707932590485522 chr21 48129895 2942236 0.06113115351695656 0.5365659654421803 chr22 51304566 4350017 0.08478810638413743 0.6063252944495658 chrMT 16571 30825 1.8601774183815099 3.6739998431530734 chrX 155270560 19787453 0.1274385369641225 0.8121706971020559 chrY 59373566 756965 0.012749192123646405 0.23091562920009162