BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549026.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 = 8,792,261 number of mapped reads = 7,705,844 (87.64%) number of secondary alignments = 0 number of mapped bases = 304,901,129 bp number of sequenced bases = 304,869,911 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 326,146 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6881 >>>>>>> ACTG content number of A's = 88,346,225 bp (28.98%) number of C's = 63,607,129 bp (20.86%) number of T's = 88,891,011 bp (29.16%) number of G's = 64,022,610 bp (21%) number of N's = 2,936 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 861,682 number of insertions = 10,239 mapped reads with insertion percentage = 0.13% number of deletions = 24,091 mapped reads with deletion percentage = 0.31% homopolymer indels = 40.98% >>>>>>> Coverage mean coverageData = 0.0985X std coverageData = 1.0263X There is a 7.48% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% 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% 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 24041580 0.096455446744905 0.8317920772903393 chr2 243199373 25735111 0.10581898580799384 0.5957456964595255 chr3 198022430 20379534 0.10291528085985006 0.40223660537530137 chr4 191154276 19741693 0.10327623013779717 0.41187242013449327 chr5 180915260 18867558 0.10428947784725291 0.4111444842021416 chr6 171115067 17686274 0.10335895202028002 0.44845471203265513 chr7 159138663 16897501 0.1061809913534337 0.8352482602856602 chr8 146364022 15957214 0.10902415622331013 3.9729156543099244 chr9 141213431 12852808 0.09101689484479702 0.5917892857040019 chr10 135534747 13968653 0.10306326096583926 0.4830329211502283 chr11 135006516 13846081 0.10255861280058512 0.7146976113182003 chr12 133851895 13804715 0.10313425147996597 0.4150722192852238 chr13 115169878 9879059 0.08577814938729031 0.36508405245895237 chr14 107349540 9304867 0.08667821958063351 0.447691012488565 chr15 102531392 8832346 0.08614284686586524 0.36767055404135224 chr16 90354753 8497444 0.0940453459044927 0.4209954018197619 chr17 81195210 8070187 0.0993924025813838 0.4368544515091087 chr18 78077248 8070656 0.10336757770970616 1.0481250949071805 chr19 59128983 6114199 0.10340443365988554 0.8225733701020708 chr20 63025520 6255488 0.09925325487199471 0.40745983856419066 chr21 48129895 3853368 0.0800618409826159 0.40491889976021156 chr22 51304566 3422558 0.06671059258156477 0.38807306199357694 chrMT 16571 27898 1.6835435399191359 2.1607990480664565 chrX 155270560 17882434 0.11516950798657517 0.5132467429924434 chrY 59373566 911903 0.015358737253544785 0.18496641296798277