BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777292.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,101,164 number of mapped reads = 1,067,910 (96.98%) number of supplementary alignments = 45,956 (4.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 536,717 number of mapped paired reads (second in pair) = 531,193 number of mapped paired reads (both in pair) = 1,059,306 number of mapped paired reads (singletons) = 8,604 number of mapped bases = 104,667,175 bp number of sequenced bases = 104,632,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,033 duplication rate = 4.66% >>>>>>> Insert size mean insert size = 211,652.7298 std insert size = 4,459,001.9635 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 53.09 >>>>>>> ACTG content number of A's = 30,366,235 bp (29.02%) number of C's = 22,029,087 bp (21.05%) number of T's = 29,803,816 bp (28.48%) number of G's = 22,431,441 bp (21.44%) number of N's = 1,720 bp (0%) GC percentage = 42.49% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 672,321 number of insertions = 24,175 mapped reads with insertion percentage = 2.21% number of deletions = 13,773 mapped reads with deletion percentage = 1.25% homopolymer indels = 45.61% >>>>>>> Coverage mean coverageData = 0.0338X std coverageData = 0.4109X There is a 2.58% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 8769564 0.035183719762928896 0.7555173890305754 chr2 243199373 9005150 0.03702785039663733 0.34858085452176285 chr3 198022430 6970483 0.03520047198693602 0.23601949497192293 chr4 191154276 6791068 0.035526633994836715 0.4121128262918542 chr5 180915260 6264867 0.03462873723311124 0.22316105499104527 chr6 171115067 6004632 0.035091193927417275 0.28886198639936367 chr7 159138663 5530820 0.034754722050165776 0.32444568959946996 chr8 146364022 5277254 0.03605567767193498 0.2579729449924645 chr9 141213431 4467459 0.03163621879564699 0.406536063581701 chr10 135534747 5713479 0.04215508662144033 0.9564433974613135 chr11 135006516 4970998 0.03682043020797603 0.28193427261949083 chr12 133851895 4739229 0.03540651404300253 0.22552239797739268 chr13 115169878 3174785 0.027566105436006454 0.19885977159529622 chr14 107349540 3170284 0.029532348252260792 0.2083372553499123 chr15 102531392 3056548 0.029810850514933027 0.20637877879599897 chr16 90354753 3338875 0.036952953653694345 0.27563316800865983 chr17 81195210 2986205 0.03677809319047269 0.2813690246898283 chr18 78077248 2912446 0.03730210880383489 0.4915328486819602 chr19 59128983 2036881 0.03444809798267628 0.4394724661687351 chr20 63025520 2392489 0.037960638801552135 0.2507406972456389 chr21 48129895 1432969 0.02977295088634621 0.2610215133921737 chr22 51304566 1327145 0.02586797050383391 0.19267104961862197 chrMT 16571 469798 28.350612515840925 8.097668139030269 chrX 155270560 2868047 0.01847128650788662 0.17552456878329414 chrY 59373566 995700 0.01677008923466042 0.3488020184494611