BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038428.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 19,193,458 number of mapped reads = 17,624,917 (91.83%) number of supplementary alignments = 254,060 (1.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,948,498 number of mapped paired reads (second in pair) = 8,676,419 number of mapped paired reads (both in pair) = 17,296,550 number of mapped paired reads (singletons) = 328,367 number of mapped bases = 2,385,006,432 bp number of sequenced bases = 2,383,340,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,567,956 duplication rate = 14.36% >>>>>>> Insert size mean insert size = 90,411.0544 std insert size = 2,918,585.9948 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 53.5713 >>>>>>> ACTG content number of A's = 679,775,638 bp (28.52%) number of C's = 476,452,802 bp (19.99%) number of T's = 689,937,069 bp (28.95%) number of G's = 536,986,066 bp (22.53%) number of N's = 189,219 bp (0.01%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 30,901,763 number of insertions = 411,815 mapped reads with insertion percentage = 2.23% number of deletions = 874,730 mapped reads with deletion percentage = 4.79% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 0.7704X std coverageData = 9.2083X There is a 28.03% of reference with a coverageData >= 1X There is a 16.62% of reference with a coverageData >= 2X There is a 9.83% of reference with a coverageData >= 3X There is a 6.24% of reference with a coverageData >= 4X There is a 3.97% of reference with a coverageData >= 5X There is a 2.6% of reference with a coverageData >= 6X There is a 1.72% of reference with a coverageData >= 7X There is a 1.16% of reference with a coverageData >= 8X There is a 0.79% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% 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 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.02% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 190187469 0.7630370918915383 14.733183583507781 chr2 243199373 208760777 0.8583935658419646 9.784042806330419 chr3 198022430 160101288 0.8085007743819728 1.7860770299503546 chr4 191154276 155227600 0.8120540290712618 8.786673206728985 chr5 180915260 142417010 0.7872028595044995 1.749804492933474 chr6 171115067 137199925 0.8017992068459991 6.970871917637943 chr7 159138663 123616411 0.7767842752329772 8.870511467581002 chr8 146364022 121448947 0.829773228013644 3.179644106490958 chr9 141213431 99693464 0.7059772097740477 15.551518539693584 chr10 135534747 127079629 0.9376166024790676 20.067944759623426 chr11 135006516 110722204 0.8201248893794134 6.928439499487694 chr12 133851895 103956466 0.7766529267292032 1.8493168223421312 chr13 115169878 72457634 0.6291370214006826 1.5396483020436569 chr14 107349540 70002376 0.6520975870040989 1.7041758180859392 chr15 102531392 66062277 0.6443126901076306 1.5922689776647971 chr16 90354753 80334684 0.8891030226157555 11.59204707759485 chr17 81195210 62945204 0.7752329724869238 13.182679585739095 chr18 78077248 66585998 0.8528220410637424 11.972950294966566 chr19 59128983 33412341 0.5650755231152885 7.099970141837635 chr20 63025520 51153838 0.8116369051774582 3.086444792723775 chr21 48129895 29811871 0.6194044470697474 4.443807049196238 chr22 51304566 24679974 0.4810482949997082 1.4395856945656695 chrMT 16571 3798773 229.24223040251042 145.14767931854087 chrX 155270560 136402057 0.8784798418966222 3.520389574708311 chrY 59373566 6948215 0.11702539476911325 9.23127480007408