BamQC report ----------------------------------- >>>>>>> Input bam file = SRR980244.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 90,113,462 number of mapped reads = 89,994,768 (99.87%) number of supplementary alignments = 466,542 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 44,997,525 number of mapped paired reads (second in pair) = 44,997,243 number of mapped paired reads (both in pair) = 89,948,772 number of mapped paired reads (singletons) = 45,996 number of mapped bases = 8,803,872,785 bp number of sequenced bases = 8,802,817,043 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,044,525 duplication rate = 61.54% >>>>>>> Insert size mean insert size = 81,904.2869 std insert size = 2,838,716.9931 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 56.4493 >>>>>>> ACTG content number of A's = 2,233,464,510 bp (25.37%) number of C's = 2,215,439,135 bp (25.17%) number of T's = 2,249,026,779 bp (25.55%) number of G's = 2,104,585,173 bp (23.91%) number of N's = 301,446 bp (0%) GC percentage = 49.08% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 35,441,451 number of insertions = 476,957 mapped reads with insertion percentage = 0.52% number of deletions = 478,910 mapped reads with deletion percentage = 0.52% homopolymer indels = 37.46% >>>>>>> Coverage mean coverageData = 2.8439X std coverageData = 25.5489X There is a 10.37% of reference with a coverageData >= 1X There is a 7.09% of reference with a coverageData >= 2X There is a 5.18% of reference with a coverageData >= 3X There is a 4.29% of reference with a coverageData >= 4X There is a 3.75% of reference with a coverageData >= 5X There is a 3.47% of reference with a coverageData >= 6X There is a 3.26% of reference with a coverageData >= 7X There is a 3.13% of reference with a coverageData >= 8X There is a 3.01% of reference with a coverageData >= 9X There is a 2.92% of reference with a coverageData >= 10X There is a 2.84% of reference with a coverageData >= 11X There is a 2.77% of reference with a coverageData >= 12X There is a 2.7% of reference with a coverageData >= 13X There is a 2.64% of reference with a coverageData >= 14X There is a 2.59% of reference with a coverageData >= 15X There is a 2.54% of reference with a coverageData >= 16X There is a 2.49% of reference with a coverageData >= 17X There is a 2.45% of reference with a coverageData >= 18X There is a 2.4% of reference with a coverageData >= 19X There is a 2.36% of reference with a coverageData >= 20X There is a 2.32% of reference with a coverageData >= 21X There is a 2.28% of reference with a coverageData >= 22X There is a 2.25% of reference with a coverageData >= 23X There is a 2.21% of reference with a coverageData >= 24X There is a 2.18% of reference with a coverageData >= 25X There is a 2.14% of reference with a coverageData >= 26X There is a 2.11% of reference with a coverageData >= 27X There is a 2.08% of reference with a coverageData >= 28X There is a 2.05% of reference with a coverageData >= 29X There is a 2.02% of reference with a coverageData >= 30X There is a 1.99% of reference with a coverageData >= 31X There is a 1.96% of reference with a coverageData >= 32X There is a 1.93% of reference with a coverageData >= 33X There is a 1.91% of reference with a coverageData >= 34X There is a 1.88% of reference with a coverageData >= 35X There is a 1.86% of reference with a coverageData >= 36X There is a 1.83% of reference with a coverageData >= 37X There is a 1.81% of reference with a coverageData >= 38X There is a 1.78% of reference with a coverageData >= 39X There is a 1.76% of reference with a coverageData >= 40X There is a 1.73% of reference with a coverageData >= 41X There is a 1.71% of reference with a coverageData >= 42X There is a 1.69% of reference with a coverageData >= 43X There is a 1.67% of reference with a coverageData >= 44X There is a 1.65% of reference with a coverageData >= 45X There is a 1.62% of reference with a coverageData >= 46X There is a 1.6% of reference with a coverageData >= 47X There is a 1.58% of reference with a coverageData >= 48X There is a 1.56% of reference with a coverageData >= 49X There is a 1.54% of reference with a coverageData >= 50X There is a 1.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 993912733 3.9876038383069865 33.11482090771286 chr2 243199373 586936752 2.4133974720403577 20.545587955258885 chr3 198022430 517678404 2.614241245297313 23.752115725669835 chr4 191154276 335190602 1.753508260521465 17.315784156440294 chr5 180915260 397704956 2.1982941405827234 19.958165077856197 chr6 171115067 743720441 4.346317679903664 44.857745568494806 chr7 159138663 452348206 2.842478361150992 26.36713451107839 chr8 146364022 292755981 2.0001908734101335 18.835741947028154 chr9 141213431 352904738 2.499087625737243 21.957046903328457 chr10 135534747 356446036 2.629923646074316 22.948148569121024 chr11 135006516 440904334 3.265800400330307 25.101451850582794 chr12 133851895 476081879 3.5567810153154724 27.414394484256064 chr13 115169878 162759325 1.4132108831442889 16.968758752104012 chr14 107349540 281715581 2.6242830756424294 22.72681972869372 chr15 102531392 301681321 2.942331271577782 23.95039836350916 chr16 90354753 358819578 3.9712307995573846 29.450735180826676 chr17 81195210 425973125 5.246283924876849 32.15605659045387 chr18 78077248 134786970 1.7263283921072627 17.797047958798633 chr19 59128983 505622419 8.551177330413411 43.222375434509885 chr20 63025520 221541566 3.5151088955711907 26.58044205333923 chr21 48129895 92379210 1.919372772369439 19.395423147160713 chr22 51304566 188464412 3.673443256492999 26.715404403876022 chrMT 16571 4553068 274.7612093416209 362.1053084009788 chrX 155270560 169423939 1.0911530105900307 10.87439065705301 chrY 59373566 9567209 0.1611358327374172 2.979032562614717