BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927044.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 30,989,054 number of mapped reads = 30,301,839 (97.78%) number of supplementary alignments = 586,199 (1.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,198,930 number of mapped paired reads (second in pair) = 15,102,909 number of mapped paired reads (both in pair) = 29,895,192 number of mapped paired reads (singletons) = 406,647 number of mapped bases = 2,779,704,550 bp number of sequenced bases = 2,777,569,837 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,918,620 duplication rate = 7.35% >>>>>>> Insert size mean insert size = 201,155.9809 std insert size = 4,436,025.3209 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 53.1197 >>>>>>> ACTG content number of A's = 786,898,392 bp (28.33%) number of C's = 548,648,879 bp (19.75%) number of T's = 804,823,576 bp (28.98%) number of G's = 636,827,022 bp (22.93%) number of N's = 371,968 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 28,798,317 number of insertions = 477,149 mapped reads with insertion percentage = 1.54% number of deletions = 1,472,372 mapped reads with deletion percentage = 4.73% homopolymer indels = 52.13% >>>>>>> Coverage mean coverageData = 0.8979X std coverageData = 3.7807X There is a 34.25% of reference with a coverageData >= 1X There is a 19.46% of reference with a coverageData >= 2X There is a 11.54% of reference with a coverageData >= 3X There is a 7.26% of reference with a coverageData >= 4X There is a 4.71% of reference with a coverageData >= 5X There is a 3.15% of reference with a coverageData >= 6X There is a 2.16% of reference with a coverageData >= 7X There is a 1.51% of reference with a coverageData >= 8X There is a 1.07% of reference with a coverageData >= 9X There is a 0.77% of reference with a coverageData >= 10X There is a 0.56% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 237214156 0.9517093881182346 3.7352189154808206 chr2 243199373 235281414 0.9674425188587966 5.565564778720038 chr3 198022430 180249918 0.9102500055170518 1.8472759480363403 chr4 191154276 156404157 0.8182090417898892 2.4187170559560047 chr5 180915260 162435101 0.8978518506399074 1.8496112742660025 chr6 171115067 151186071 0.8835345341038846 1.8382501120666812 chr7 159138663 138859118 0.8725668255739965 2.158968129684388 chr8 146364022 132870632 0.9078093795482062 2.2099855730937294 chr9 141213431 121660379 0.8615354654190082 3.6987083546432213 chr10 135534747 135342073 0.9985784162049604 4.214800000302066 chr11 135006516 133557830 0.9892695105175516 2.939728258927015 chr12 133851895 124185089 0.9277798345701419 1.9366143876805464 chr13 115169878 79578527 0.6909664955970518 1.599570849130586 chr14 107349540 84683145 0.7888542885232671 1.8385165973870892 chr15 102531392 87067175 0.8491757821838604 1.9223379182904166 chr16 90354753 91350772 1.01102342673661 4.733973854010471 chr17 81195210 87635246 1.0793154670084601 2.698268343597227 chr18 78077248 69602937 0.8914624782881692 3.692657929716623 chr19 59128983 58564978 0.9904614459545161 2.6729264812326674 chr20 63025520 70875179 1.1245473103593593 2.319651497379383 chr21 48129895 34006910 0.7065652231321095 2.2623320482965066 chr22 51304566 43957184 0.8567889259603132 2.137370198732761 chrMT 16571 12739114 768.7595196427494 598.4950314569351 chrX 155270560 145694750 0.9383282317008453 2.116321533354363 chrY 59373566 4702695 0.07920519714109811 2.4825177874529363