BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618660.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 35,446,248 number of mapped reads = 32,955,624 (92.97%) number of supplementary alignments = 101,478 (0.29%) number of secondary alignments = 0 number of mapped bases = 3,214,680,781 bp number of sequenced bases = 3,212,403,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,226,387 duplication rate = 34.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.7327 >>>>>>> ACTG content number of A's = 876,555,641 bp (27.29%) number of C's = 709,068,663 bp (22.07%) number of T's = 892,643,705 bp (27.79%) number of G's = 702,243,146 bp (21.86%) number of N's = 31,892,053 bp (0.99%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.0199 number of mismatches = 63,049,246 number of insertions = 597,922 mapped reads with insertion percentage = 1.79% number of deletions = 1,638,293 mapped reads with deletion percentage = 4.85% homopolymer indels = 53.05% >>>>>>> Coverage mean coverageData = 1.0384X std coverageData = 4.3167X There is a 20.48% of reference with a coverageData >= 1X There is a 13.95% of reference with a coverageData >= 2X There is a 10.52% of reference with a coverageData >= 3X There is a 8.3% of reference with a coverageData >= 4X There is a 6.71% of reference with a coverageData >= 5X There is a 5.52% of reference with a coverageData >= 6X There is a 4.6% of reference with a coverageData >= 7X There is a 3.87% of reference with a coverageData >= 8X There is a 3.28% of reference with a coverageData >= 9X There is a 2.81% of reference with a coverageData >= 10X There is a 2.41% of reference with a coverageData >= 11X There is a 2.09% of reference with a coverageData >= 12X There is a 1.82% of reference with a coverageData >= 13X There is a 1.6% of reference with a coverageData >= 14X There is a 1.4% of reference with a coverageData >= 15X There is a 1.24% of reference with a coverageData >= 16X There is a 1.1% of reference with a coverageData >= 17X There is a 0.98% of reference with a coverageData >= 18X There is a 0.88% of reference with a coverageData >= 19X There is a 0.79% of reference with a coverageData >= 20X There is a 0.71% of reference with a coverageData >= 21X There is a 0.64% of reference with a coverageData >= 22X There is a 0.58% of reference with a coverageData >= 23X There is a 0.52% of reference with a coverageData >= 24X There is a 0.48% of reference with a coverageData >= 25X There is a 0.43% of reference with a coverageData >= 26X There is a 0.4% of reference with a coverageData >= 27X There is a 0.36% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 302416038 1.2133010412840657 5.053264787092601 chr2 243199373 276768337 1.1380306354654952 4.8931475199101255 chr3 198022430 212269242 1.0719454457760165 3.788526874525104 chr4 191154276 169511256 0.886777212349673 3.8236278463353055 chr5 180915260 190601323 1.0535392260442817 3.7114993793034015 chr6 171115067 180810847 1.0566623393835914 3.77223845701761 chr7 159138663 168061422 1.0560690836016386 3.882485165096911 chr8 146364022 166531772 1.1377917176941201 3.9523755097416418 chr9 141213431 145926050 1.0333723142807854 4.299620106280117 chr10 135534747 165088223 1.2180509179686594 4.145426295577582 chr11 135006516 170291998 1.2613613257007537 4.951335599924277 chr12 133851895 152102957 1.1363526605282652 4.0098383411707665 chr13 115169878 90770370 0.7881433199052273 3.1063101242278575 chr14 107349540 103196815 0.9613158565933305 3.648143669890709 chr15 102531392 108212553 1.0554089912287545 3.909060533777785 chr16 90354753 114320481 1.2652403687053408 7.6742771246842025 chr17 81195210 105061503 1.2939372039311186 4.621486865266214 chr18 78077248 85287331 1.0923455063375185 5.070096932536687 chr19 59128983 70245405 1.1880029291219163 4.585976197222612 chr20 63025520 97710930 1.5503391324657059 4.970211614037048 chr21 48129895 42416002 0.8812818311778989 6.124525969339482 chr22 51304566 59082284 1.1515989434546625 4.458386983873757 chrMT 16571 25743 1.553497073200169 6.315656128173825 chrX 155270560 9074406 0.05844254055630378 1.2502870600424112 chrY 59373566 28897493 0.4867063736747764 3.108598417030845