BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506105.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,883,100 number of mapped reads = 7,730,030 (87.02%) number of supplementary alignments = 147,582 (1.66%) number of secondary alignments = 0 number of mapped bases = 627,677,736 bp number of sequenced bases = 627,387,062 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,633,883 duplication rate = 13.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2547 >>>>>>> ACTG content number of A's = 169,886,535 bp (27.08%) number of C's = 119,482,325 bp (19.04%) number of T's = 190,297,243 bp (30.33%) number of G's = 147,611,671 bp (23.53%) number of N's = 109,288 bp (0.02%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 4,841,677 number of insertions = 55,166 mapped reads with insertion percentage = 0.7% number of deletions = 144,587 mapped reads with deletion percentage = 1.84% homopolymer indels = 43.47% >>>>>>> Coverage mean coverageData = 0.2028X std coverageData = 1.7994X There is a 9.8% of reference with a coverageData >= 1X There is a 4.34% of reference with a coverageData >= 2X There is a 2.24% of reference with a coverageData >= 3X There is a 1.26% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.12% 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 0.04% of reference with a coverageData >= 12X There is a 0.03% 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 0.01% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 47101512 0.1889724960805614 3.913933086147202 chr2 243199373 49953656 0.20540207560485774 1.6495749181213484 chr3 198022430 38699725 0.1954310175872501 0.8043116184668173 chr4 191154276 38643230 0.2021572878652215 1.5005880181688949 chr5 180915260 46711070 0.25819308995824897 0.9287421201543917 chr6 171115067 24988003 0.1460304077138923 0.85962416245757 chr7 159138663 31797174 0.19980797501107572 1.6912908920688032 chr8 146364022 41128034 0.28099824969281045 1.96047357030429 chr9 141213431 18962594 0.13428321842842272 1.5485058282684931 chr10 135534747 37193087 0.27441735660597794 2.3395777497355907 chr11 135006516 25701863 0.1903749816045916 1.4992616392681528 chr12 133851895 26754635 0.19988237745905651 0.8552525355657612 chr13 115169878 12267467 0.10651628023778927 0.5737072010414975 chr14 107349540 19014997 0.17713161136973665 0.9387819072113336 chr15 102531392 24341526 0.23740559379121665 0.9050646212774361 chr16 90354753 23622624 0.26144306985156607 1.2555472262657195 chr17 81195210 15914251 0.19599987486946582 1.060997013773305 chr18 78077248 7985294 0.10227427585562442 3.0298125947488326 chr19 59128983 15185051 0.25681231486765127 2.6349315241747613 chr20 63025520 16070706 0.2549872813425419 1.042488077702861 chr21 48129895 10661371 0.22151245083746807 1.3429854873635976 chr22 51304566 7687380 0.14983812551888656 0.8354903193900578 chrMT 16571 32845 1.9820771226842073 2.677465818138544 chrX 155270560 44544329 0.28688200132723163 1.220046369337567 chrY 59373566 2715312 0.045732675042627555 1.8054999718665212