BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927014.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 = 28,998,104 number of mapped reads = 27,624,518 (95.26%) number of supplementary alignments = 280,697 (0.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,850,049 number of mapped paired reads (second in pair) = 13,774,469 number of mapped paired reads (both in pair) = 27,338,834 number of mapped paired reads (singletons) = 285,684 number of mapped bases = 2,610,457,866 bp number of sequenced bases = 2,608,496,746 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,876,894 duplication rate = 5.31% >>>>>>> Insert size mean insert size = 104,190.961 std insert size = 3,179,847.7361 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.4716 >>>>>>> ACTG content number of A's = 741,781,251 bp (28.44%) number of C's = 527,728,060 bp (20.23%) number of T's = 749,359,098 bp (28.73%) number of G's = 589,060,643 bp (22.58%) number of N's = 567,694 bp (0.02%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 23,950,895 number of insertions = 412,452 mapped reads with insertion percentage = 1.47% number of deletions = 1,380,020 mapped reads with deletion percentage = 4.87% homopolymer indels = 52.89% >>>>>>> Coverage mean coverageData = 0.8433X std coverageData = 3.3596X There is a 33.28% of reference with a coverageData >= 1X There is a 18.66% of reference with a coverageData >= 2X There is a 10.89% of reference with a coverageData >= 3X There is a 6.75% of reference with a coverageData >= 4X There is a 4.32% of reference with a coverageData >= 5X There is a 2.83% of reference with a coverageData >= 6X There is a 1.9% of reference with a coverageData >= 7X There is a 1.29% of reference with a coverageData >= 8X There is a 0.89% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 214730793 0.8615055486662158 4.262854680717473 chr2 243199373 226945257 0.9331654691395935 5.187274906185708 chr3 198022430 174436844 0.8808943714103499 1.796464157497588 chr4 191154276 153403718 0.8025126155169032 2.2986239327250297 chr5 180915260 157196565 0.8688961063870455 1.7514208608855972 chr6 171115067 149573468 0.87411044873097 1.997345684868037 chr7 159138663 136036264 0.8548284963283875 2.4765217990939274 chr8 146364022 131483180 0.8983299188102387 1.990485589849678 chr9 141213431 111256442 0.7878602000683632 3.827733292970151 chr10 135534747 131120420 0.9674302929860488 7.884017468663215 chr11 135006516 125644651 0.9306561988459876 3.6047121202786316 chr12 133851895 116811060 0.872688877508981 1.7879392917372936 chr13 115169878 78272425 0.6796258393188538 1.5385688055808349 chr14 107349540 78555320 0.7317713704222673 1.6744624240717814 chr15 102531392 78227035 0.762956919574446 1.717006855458589 chr16 90354753 83575876 0.9249748709954417 4.577571854239922 chr17 81195210 70459903 0.8677839862720966 2.17976638605104 chr18 78077248 69842487 0.8945305935987907 4.271149239525765 chr19 59128983 43327589 0.7327639814133113 2.5740343320622054 chr20 63025520 62731539 0.995335524403448 2.074189780310034 chr21 48129895 33643920 0.6990233408986244 2.5555817861896553 chr22 51304566 34889975 0.6800559427790501 1.7344496086018648 chrMT 16571 311785 18.81509866634482 14.740375003121516 chrX 155270560 143536462 0.9244280564197103 2.128362168578032 chrY 59373566 4444888 0.07486307964052555 2.141450871004069