BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617397.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,291,123 (94.66%) number of supplementary alignments = 459,516 (1.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,205,088 number of mapped paired reads (second in pair) = 15,086,035 number of mapped paired reads (both in pair) = 29,843,964 number of mapped paired reads (singletons) = 447,159 number of mapped bases = 2,986,785,001 bp number of sequenced bases = 2,986,133,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,395,928 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 47,364.9619 std insert size = 2,064,302.214 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.9702 >>>>>>> ACTG content number of A's = 889,355,917 bp (29.78%) number of C's = 600,844,915 bp (20.12%) number of T's = 880,678,268 bp (29.49%) number of G's = 613,195,839 bp (20.53%) number of N's = 2,058,708 bp (0.07%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 29,805,836 number of insertions = 745,219 mapped reads with insertion percentage = 2.44% number of deletions = 289,718 mapped reads with deletion percentage = 0.94% homopolymer indels = 35.9% >>>>>>> Coverage mean coverageData = 0.9648X std coverageData = 2.9499X There is a 29.76% of reference with a coverageData >= 1X There is a 17.12% of reference with a coverageData >= 2X There is a 10.99% of reference with a coverageData >= 3X There is a 7.61% of reference with a coverageData >= 4X There is a 5.54% of reference with a coverageData >= 5X There is a 4.18% of reference with a coverageData >= 6X There is a 3.24% of reference with a coverageData >= 7X There is a 2.57% of reference with a coverageData >= 8X There is a 2.07% of reference with a coverageData >= 9X There is a 1.69% of reference with a coverageData >= 10X There is a 1.4% of reference with a coverageData >= 11X There is a 1.18% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.85% of reference with a coverageData >= 14X There is a 0.73% of reference with a coverageData >= 15X There is a 0.63% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192215461 0.7711734487514075 2.7654264637512367 chr2 243199373 297326109 1.222561165895769 3.08542060419602 chr3 198022430 252267810 1.2739355334645677 3.4554160489317707 chr4 191154276 143171709 0.7489851234089056 2.2902673630965475 chr5 180915260 191153837 1.0565932193890113 2.8913899419248916 chr6 171115067 136657986 0.7986321040916871 2.6061884344374544 chr7 159138663 223578415 1.4049283234206889 3.25481048974186 chr8 146364022 131894623 0.9011410126458537 3.296929625242636 chr9 141213431 119531698 0.8464612548079793 2.6402566921155723 chr10 135534747 95718267 0.7062267729765268 2.437105259398612 chr11 135006516 221997892 1.6443494623622463 3.878293039644407 chr12 133851895 142322489 1.0632833326715323 2.804619093554036 chr13 115169878 129414212 1.1236810722331407 2.7829453396745802 chr14 107349540 86753782 0.808143025112171 2.9254015245228615 chr15 102531392 68637719 0.669431260623088 2.3656735886544973 chr16 90354753 75268384 0.8330318162675958 3.366481567815365 chr17 81195210 92362063 1.1375309331671166 3.7314857173419584 chr18 78077248 42881146 0.5492143626783567 2.020953536300475 chr19 59128983 42796533 0.7237826667845784 2.3633980689526513 chr20 63025520 102271627 1.6227018357008398 4.797083056513233 chr21 48129895 40907612 0.8499418500705227 2.5561363377623376 chr22 51304566 24197334 0.4716409451743535 2.1027016189138577 chrMT 16571 181245 10.937481141753667 5.504149197750309 chrX 155270560 130919474 0.8431699737542004 2.5749641326740447 chrY 59373566 2357574 0.039707468471743806 0.5656963566511587