BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104295.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 640,573,026 number of mapped reads = 598,815,986 (93.48%) number of supplementary alignments = 304,734 (0.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 309,780,312 number of mapped paired reads (second in pair) = 289,035,674 number of mapped paired reads (both in pair) = 577,253,112 number of mapped paired reads (singletons) = 21,562,874 number of mapped bases = 34,365,089,077 bp number of sequenced bases = 34,360,943,719 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 392,759,896 duplication rate = 51.6% >>>>>>> Insert size mean insert size = 14,660.2476 std insert size = 1,103,662.9444 median insert size = 54 >>>>>>> Mapping quality mean mapping quality = 50.4074 >>>>>>> ACTG content number of A's = 9,219,411,007 bp (26.83%) number of C's = 8,114,553,064 bp (23.62%) number of T's = 9,850,024,547 bp (28.67%) number of G's = 7,169,036,365 bp (20.86%) number of N's = 7,918,736 bp (0.02%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 139,495,456 number of insertions = 1,811,001 mapped reads with insertion percentage = 0.3% number of deletions = 2,036,046 mapped reads with deletion percentage = 0.34% homopolymer indels = 36% >>>>>>> Coverage mean coverageData = 11.1009X std coverageData = 119.632X There is a 84.28% of reference with a coverageData >= 1X There is a 79.76% of reference with a coverageData >= 2X There is a 72.3% of reference with a coverageData >= 3X There is a 67.82% of reference with a coverageData >= 4X There is a 61.33% of reference with a coverageData >= 5X There is a 57.21% of reference with a coverageData >= 6X There is a 51.74% of reference with a coverageData >= 7X There is a 48.1% of reference with a coverageData >= 8X There is a 43.57% of reference with a coverageData >= 9X There is a 40.42% of reference with a coverageData >= 10X There is a 36.69% of reference with a coverageData >= 11X There is a 34% of reference with a coverageData >= 12X There is a 30.92% of reference with a coverageData >= 13X There is a 28.63% of reference with a coverageData >= 14X There is a 26.08% of reference with a coverageData >= 15X There is a 24.13% of reference with a coverageData >= 16X There is a 22% of reference with a coverageData >= 17X There is a 20.34% of reference with a coverageData >= 18X There is a 18.56% of reference with a coverageData >= 19X There is a 17.13% of reference with a coverageData >= 20X There is a 15.63% of reference with a coverageData >= 21X There is a 14.41% of reference with a coverageData >= 22X There is a 13.15% of reference with a coverageData >= 23X There is a 12.11% of reference with a coverageData >= 24X There is a 11.05% of reference with a coverageData >= 25X There is a 10.16% of reference with a coverageData >= 26X There is a 9.27% of reference with a coverageData >= 27X There is a 8.52% of reference with a coverageData >= 28X There is a 7.77% of reference with a coverageData >= 29X There is a 7.13% of reference with a coverageData >= 30X There is a 6.5% of reference with a coverageData >= 31X There is a 5.96% of reference with a coverageData >= 32X There is a 5.43% of reference with a coverageData >= 33X There is a 4.98% of reference with a coverageData >= 34X There is a 4.54% of reference with a coverageData >= 35X There is a 4.16% of reference with a coverageData >= 36X There is a 3.79% of reference with a coverageData >= 37X There is a 3.47% of reference with a coverageData >= 38X There is a 3.17% of reference with a coverageData >= 39X There is a 2.9% of reference with a coverageData >= 40X There is a 2.65% of reference with a coverageData >= 41X There is a 2.43% of reference with a coverageData >= 42X There is a 2.22% of reference with a coverageData >= 43X There is a 2.04% of reference with a coverageData >= 44X There is a 1.86% of reference with a coverageData >= 45X There is a 1.71% of reference with a coverageData >= 46X There is a 1.56% of reference with a coverageData >= 47X There is a 1.44% of reference with a coverageData >= 48X There is a 1.32% of reference with a coverageData >= 49X There is a 1.21% of reference with a coverageData >= 50X There is a 1.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2659056363 10.668203562870962 246.96303438851837 chr2 243199373 2991017091 12.298621719719648 60.25090953574985 chr3 198022430 2364082891 11.93846015827601 31.184344802469855 chr4 191154276 2521864353 13.192822079480974 36.87707984845452 chr5 180915260 2204734361 12.186558287012383 30.313873098687925 chr6 171115067 2118366983 12.37978057770915 40.63286558423726 chr7 159138663 1891499091 11.8858551111492 96.83985321145235 chr8 146364022 1778880222 12.153808003445 72.78165390589581 chr9 141213431 1438100249 10.183877261646593 51.213795441961175 chr10 135534747 1652287030 12.190874049442096 175.02355988200375 chr11 135006516 1526369024 11.305891517117589 48.65732270682134 chr12 133851895 1498397033 11.194440190779519 22.022216538092113 chr13 115169878 1170218879 10.16080679533237 21.92847656701748 chr14 107349540 983902191 9.16540667989821 23.85345521678206 chr15 102531392 789080653 7.695990833714615 12.49880668735164 chr16 90354753 923678565 10.222799956079786 76.53987510759241 chr17 81195210 727343868 8.957965229722296 29.21272079198974 chr18 78077248 929966196 11.910847523724197 99.33712305962823 chr19 59128983 549682680 9.296332392525676 166.8803327395022 chr20 63025520 599456228 9.511325380575995 19.36953734011329 chr21 48129895 442781853 9.199726136946694 37.00117183881917 chr22 51304566 303207468 5.909950938869652 87.7927819178776 chrMT 16571 476966194 28783.187134150023 12198.606632987943 chrX 155270560 1717131469 11.05896358588518 28.754682129535716 chrY 59373566 107018142 1.8024543447499852 56.28346329714008