BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504610.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 = 442,742,124 number of mapped reads = 295,108,901 (66.65%) number of supplementary alignments = 1,869,649 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 147,727,565 number of mapped paired reads (second in pair) = 147,381,336 number of mapped paired reads (both in pair) = 293,366,614 number of mapped paired reads (singletons) = 1,742,287 number of mapped bases = 29,307,463,684 bp number of sequenced bases = 29,299,997,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,026,902 duplication rate = 22.73% >>>>>>> Insert size mean insert size = 24,297.8467 std insert size = 1,504,855.5067 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.777 >>>>>>> ACTG content number of A's = 7,567,261,144 bp (25.83%) number of C's = 7,018,702,208 bp (23.95%) number of T's = 7,616,691,570 bp (26%) number of G's = 7,092,314,858 bp (24.21%) number of N's = 5,028,196 bp (0.02%) GC percentage = 48.16% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 144,658,587 number of insertions = 2,189,914 mapped reads with insertion percentage = 0.72% number of deletions = 2,883,080 mapped reads with deletion percentage = 0.95% homopolymer indels = 39.92% >>>>>>> Coverage mean coverageData = 9.4672X std coverageData = 24.3124X There is a 68.17% of reference with a coverageData >= 1X There is a 58.32% of reference with a coverageData >= 2X There is a 50.85% of reference with a coverageData >= 3X There is a 45.08% of reference with a coverageData >= 4X There is a 40.33% of reference with a coverageData >= 5X There is a 36.36% of reference with a coverageData >= 6X There is a 32.98% of reference with a coverageData >= 7X There is a 30.08% of reference with a coverageData >= 8X There is a 27.55% of reference with a coverageData >= 9X There is a 25.33% of reference with a coverageData >= 10X There is a 23.37% of reference with a coverageData >= 11X There is a 21.63% of reference with a coverageData >= 12X There is a 20.08% of reference with a coverageData >= 13X There is a 18.7% of reference with a coverageData >= 14X There is a 17.44% of reference with a coverageData >= 15X There is a 16.31% of reference with a coverageData >= 16X There is a 15.29% of reference with a coverageData >= 17X There is a 14.35% of reference with a coverageData >= 18X There is a 13.5% of reference with a coverageData >= 19X There is a 12.72% of reference with a coverageData >= 20X There is a 12.01% of reference with a coverageData >= 21X There is a 11.35% of reference with a coverageData >= 22X There is a 10.74% of reference with a coverageData >= 23X There is a 10.18% of reference with a coverageData >= 24X There is a 9.66% of reference with a coverageData >= 25X There is a 9.17% of reference with a coverageData >= 26X There is a 8.73% of reference with a coverageData >= 27X There is a 8.31% of reference with a coverageData >= 28X There is a 7.92% of reference with a coverageData >= 29X There is a 7.56% of reference with a coverageData >= 30X There is a 7.22% of reference with a coverageData >= 31X There is a 6.9% of reference with a coverageData >= 32X There is a 6.6% of reference with a coverageData >= 33X There is a 6.32% of reference with a coverageData >= 34X There is a 6.06% of reference with a coverageData >= 35X There is a 5.81% of reference with a coverageData >= 36X There is a 5.57% of reference with a coverageData >= 37X There is a 5.35% of reference with a coverageData >= 38X There is a 5.15% of reference with a coverageData >= 39X There is a 4.95% of reference with a coverageData >= 40X There is a 4.76% of reference with a coverageData >= 41X There is a 4.59% of reference with a coverageData >= 42X There is a 4.42% of reference with a coverageData >= 43X There is a 4.26% of reference with a coverageData >= 44X There is a 4.11% of reference with a coverageData >= 45X There is a 3.97% of reference with a coverageData >= 46X There is a 3.83% of reference with a coverageData >= 47X There is a 3.7% of reference with a coverageData >= 48X There is a 3.58% of reference with a coverageData >= 49X There is a 3.46% of reference with a coverageData >= 50X There is a 3.35% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2970530031 11.91784405223207 23.7352852079455 chr2 243199373 1309075589 5.382726003162845 13.437609493908017 chr3 198022430 1655653720 8.360940323780493 22.636962117371063 chr4 191154276 989083047 5.174265874125672 9.821072537697688 chr5 180915260 1429415028 7.901019670756353 22.548712113030824 chr6 171115067 1242523603 7.261333702426099 14.079195931247883 chr7 159138663 2344630895 14.733257467420096 27.194997976350443 chr8 146364022 2642930278 18.057240036762586 43.08197036594286 chr9 141213431 894985099 6.33781852520813 17.68390850160434 chr10 135534747 1440980674 10.631817344964682 21.978101170762564 chr11 135006516 1651000676 12.229044381828208 28.05639926124756 chr12 133851895 884095180 6.605025502253816 16.32934650205022 chr13 115169878 801619735 6.960324599805515 15.51345274693684 chr14 107349540 1038234728 9.671534018683266 19.320289799443902 chr15 102531392 893016768 8.70969125241175 18.136500440042045 chr16 90354753 1092380624 12.089907699708947 27.284792097926417 chr17 81195210 1421647106 17.509002144338318 56.36243075125064 chr18 78077248 669476465 8.57453973019131 24.518956059581758 chr19 59128983 615429439 10.4082534110218 22.287454051007014 chr20 63025520 1663227751 26.389750548666637 47.11249415013494 chr21 48129895 244440594 5.078768486820925 13.134435222846658 chr22 51304566 322103799 6.278267688688761 16.213266537147522 chrMT 16571 505992 30.534789692836885 13.417563395481087 chrX 155270560 1062291007 6.8415481144654855 12.786451976312135 chrY 59373566 28185856 0.47472061893671674 10.884438421277082