BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038487.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 = 16,292,648 number of mapped reads = 15,576,459 (95.6%) number of supplementary alignments = 222,564 (1.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,859,907 number of mapped paired reads (second in pair) = 7,716,552 number of mapped paired reads (both in pair) = 15,412,904 number of mapped paired reads (singletons) = 163,555 number of mapped bases = 2,249,072,796 bp number of sequenced bases = 2,247,576,248 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,474,054 duplication rate = 10.22% >>>>>>> Insert size mean insert size = 62,844.8467 std insert size = 2,372,818.8724 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 53.7038 >>>>>>> ACTG content number of A's = 654,075,705 bp (29.1%) number of C's = 466,719,719 bp (20.77%) number of T's = 649,954,254 bp (28.92%) number of G's = 476,777,210 bp (21.21%) number of N's = 49,360 bp (0%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 30,552,283 number of insertions = 378,204 mapped reads with insertion percentage = 2.3% number of deletions = 760,693 mapped reads with deletion percentage = 4.7% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.7265X std coverageData = 11.53X There is a 27.61% of reference with a coverageData >= 1X There is a 16.05% of reference with a coverageData >= 2X There is a 8.78% of reference with a coverageData >= 3X There is a 5.43% of reference with a coverageData >= 4X There is a 3.26% of reference with a coverageData >= 5X There is a 2.07% of reference with a coverageData >= 6X There is a 1.32% of reference with a coverageData >= 7X There is a 0.87% of reference with a coverageData >= 8X There is a 0.58% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% 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 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% 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 144099024 0.5781290470686531 18.055287467581593 chr2 243199373 239988645 0.9867979593845416 11.964105684881925 chr3 198022430 121689698 0.6145248192338615 1.489227158807573 chr4 191154276 123012795 0.6435262531087717 8.194368039523992 chr5 180915260 130100487 0.7191238981167205 1.6886835474128938 chr6 171115067 173014106 1.011098023296803 19.765329016467224 chr7 159138663 119224716 0.7491876188503607 8.533083296959777 chr8 146364022 103805853 0.7092306673562169 2.939024479685899 chr9 141213431 82950392 0.5874114906251375 16.50473144212067 chr10 135534747 103890451 0.7665226320155377 22.758732833000042 chr11 135006516 129986854 0.9628191131159921 11.340059940824316 chr12 133851895 74437889 0.5561212936133627 1.3999720119949635 chr13 115169878 148927913 1.2931151407488684 2.4233072951966617 chr14 107349540 40013377 0.3727391565907036 1.3062902230043643 chr15 102531392 38461832 0.3751224990683829 1.0566948208423996 chr16 90354753 92049019 1.0187512659129287 15.429439721389969 chr17 81195210 65668496 0.8087730298375976 14.303628561402581 chr18 78077248 33538989 0.4295616182578566 15.044665406852111 chr19 59128983 29633963 0.5011749145085076 10.641481702128816 chr20 63025520 71498023 1.1344297198975908 3.261345364122753 chr21 48129895 19015886 0.3950951066899273 3.9073696618359186 chr22 51304566 13970265 0.27230061745381495 0.9300033373639784 chrMT 16571 3040721 183.49653008267455 132.3208560276899 chrX 155270560 116009860 0.7471465292583475 3.1613474493944493 chrY 59373566 31043542 0.5228512297880171 11.764748047660627