BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548991.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,665,980 number of mapped reads = 7,487,346 (86.4%) number of secondary alignments = 0 number of mapped bases = 297,228,262 bp number of sequenced bases = 297,197,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 668,663 duplication rate = 8.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6703 >>>>>>> ACTG content number of A's = 89,675,592 bp (30.17%) number of C's = 58,288,205 bp (19.61%) number of T's = 90,190,967 bp (30.35%) number of G's = 59,039,910 bp (19.87%) number of N's = 3,016 bp (0%) GC percentage = 39.48% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 839,901 number of insertions = 9,188 mapped reads with insertion percentage = 0.12% number of deletions = 23,949 mapped reads with deletion percentage = 0.32% homopolymer indels = 43.91% >>>>>>> Coverage mean coverageData = 0.096X std coverageData = 0.7575X There is a 7.02% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 24154929 0.09691020589272674 1.1035153797900035 chr2 243199373 25414853 0.10450213208403296 0.5327401802449957 chr3 198022430 20743594 0.10475375946048132 0.41666342530358913 chr4 191154276 20672056 0.10814330933407945 0.45229669064838907 chr5 180915260 19658699 0.10866246993205549 0.42836405809802736 chr6 171115067 18275988 0.10680525286531314 0.47745272648851145 chr7 159138663 16423408 0.1032018724450387 0.7342050190673034 chr8 146364022 15958352 0.10903193135810384 2.2917101718704505 chr9 141213431 12696590 0.08991064029879707 0.49844122425471865 chr10 135534747 13936026 0.10282253302911319 0.5636887398766823 chr11 135006516 14362134 0.10638104311942988 0.5325890188306767 chr12 133851895 14129563 0.10556117266774595 0.43208009003926034 chr13 115169878 10174747 0.08834555681304099 0.38107161758059976 chr14 107349540 8946672 0.08334150290723183 0.44202318128557905 chr15 102531392 8154193 0.07952874569380664 0.3593412462757407 chr16 90354753 7583236 0.08392736129775044 0.40175116898647517 chr17 81195210 7066103 0.08702610658929265 0.41451622869339166 chr18 78077248 8184536 0.10482613321617074 0.9947957578629993 chr19 59128983 4836394 0.08179396557522392 0.8572272724849105 chr20 63025520 5742451 0.09111310783314441 0.4032684954354009 chr21 48129895 4008776 0.08329076969729521 0.4267245528346458 chr22 51304566 2794195 0.05446289127560303 0.32426945450459843 chrMT 16571 10309 0.6221109166616378 1.1518677448079204 chrX 155270560 10648234 0.06857857664711198 0.40751882382161286 chrY 59373566 2652224 0.04467011464327408 0.42875147629627147