BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124915.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,236,102 number of mapped reads = 4,179,243 (98.66%) number of supplementary alignments = 17,047 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,093,499 number of mapped paired reads (second in pair) = 2,085,744 number of mapped paired reads (both in pair) = 4,163,780 number of mapped paired reads (singletons) = 15,463 number of mapped bases = 362,422,271 bp number of sequenced bases = 362,222,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 272,174 duplication rate = 4.75% >>>>>>> Insert size mean insert size = 33,384.5687 std insert size = 1,740,120.6352 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.7002 >>>>>>> ACTG content number of A's = 101,756,942 bp (28.09%) number of C's = 67,389,732 bp (18.6%) number of T's = 107,628,730 bp (29.71%) number of G's = 85,309,598 bp (23.55%) number of N's = 137,688 bp (0.04%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 2,602,443 number of insertions = 49,060 mapped reads with insertion percentage = 1.14% number of deletions = 116,031 mapped reads with deletion percentage = 2.72% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.1171X std coverageData = 0.8953X There is a 8.43% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 32448373 0.13018371978298904 1.0460480284512021 chr2 243199373 33635217 0.1383030580428347 1.2866237172746975 chr3 198022430 26239092 0.13250565605118572 0.46047166754099744 chr4 191154276 17631804 0.09223860626586244 0.634388808966275 chr5 180915260 20361861 0.11254916251951327 0.4356826079755472 chr6 171115067 21009219 0.12277831150894503 0.7344542152152718 chr7 159138663 18489545 0.11618512215350207 1.0434287901172459 chr8 146364022 23308798 0.15925223754783124 0.780822394116682 chr9 141213431 14401076 0.10198092276364279 1.086936587473555 chr10 135534747 17036206 0.12569622459988064 1.6128655826617668 chr11 135006516 15396015 0.1140390512706809 0.8188894523477536 chr12 133851895 22202870 0.16587639644548924 0.5426300501620488 chr13 115169878 7272352 0.06314456632488574 0.3086242871063398 chr14 107349540 9282924 0.08647381255662577 0.3958692388012475 chr15 102531392 6639944 0.06476010781166416 0.3235729804748783 chr16 90354753 10122369 0.11202918124296128 0.8570164283535303 chr17 81195210 13575679 0.16719802806101494 1.8022523373521655 chr18 78077248 7407699 0.09487653816896825 1.156427570081535 chr19 59128983 6674266 0.11287638754077675 0.6109200247046281 chr20 63025520 7416325 0.11767177803531013 0.46357992401555786 chr21 48129895 3991468 0.08293115952154062 0.46398032734997624 chr22 51304566 4459754 0.08692703881366037 0.39882262056159146 chrMT 16571 267988 16.172107899342226 9.765900513050994 chrX 155270560 22187091 0.1428930957678004 0.5816892113885437 chrY 59373566 964336 0.016241840687150236 1.0070048670095566