BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013328.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,269,271 number of mapped reads = 1,996,400 (87.98%) number of supplementary alignments = 11,553 (0.51%) number of secondary alignments = 0 number of mapped bases = 130,917,111 bp number of sequenced bases = 130,850,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,427 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0882 >>>>>>> ACTG content number of A's = 36,728,639 bp (28.07%) number of C's = 23,865,808 bp (18.24%) number of T's = 41,312,434 bp (31.57%) number of G's = 28,941,526 bp (22.12%) number of N's = 1,713 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,026,912 number of insertions = 9,644 mapped reads with insertion percentage = 0.48% number of deletions = 39,061 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.0423X std coverageData = 0.4781X There is a 3.63% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 9971513 0.040005970536779525 0.8613924842554087 chr2 243199373 11309820 0.04650431397288183 0.5584617720234046 chr3 198022430 6099445 0.030801788464064398 0.19566747176556656 chr4 191154276 7514466 0.03931100134009035 0.23672281021306513 chr5 180915260 7898120 0.04365646104148428 0.24092626816128285 chr6 171115067 7886721 0.04609016107272424 0.38991411686993777 chr7 159138663 8388554 0.05271223121938633 0.8927615164068907 chr8 146364022 9640666 0.0658677308006745 0.5931080028270926 chr9 141213431 4261174 0.030175415821459647 0.4375762348293203 chr10 135534747 5006376 0.03693795215480795 0.35078714555207036 chr11 135006516 6106037 0.045227720712383984 0.4363087133344288 chr12 133851895 5467620 0.04084828234968209 0.23484164350442782 chr13 115169878 2330660 0.0202367150202243 0.1604209798904819 chr14 107349540 5411217 0.050407454004926334 0.26799922769900303 chr15 102531392 3141454 0.03063894811844552 0.2093684047758869 chr16 90354753 4993095 0.05526101100625 0.29809601430921356 chr17 81195210 3658253 0.04505503465044305 0.3391881779288923 chr18 78077248 2702425 0.03461219586018196 0.8346296077164987 chr19 59128983 2330825 0.039419331802138385 0.5913124119722145 chr20 63025520 4296747 0.06817471716219081 0.3008108713388042 chr21 48129895 2447953 0.050861382514962895 0.27119011068453824 chr22 51304566 1450975 0.02828159583301026 0.18491277402103468 chrMT 16571 14232 0.8588497978395992 1.17669621173964 chrX 155270560 8275153 0.05329505477406664 0.33203501270705815 chrY 59373566 313610 0.00528198019974074 0.10526369240811663