BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960914.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 199,914,520 number of mapped reads = 189,756,385 (94.92%) number of supplementary alignments = 3,091,871 (1.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 95,574,351 number of mapped paired reads (second in pair) = 94,182,034 number of mapped paired reads (both in pair) = 184,211,690 number of mapped paired reads (singletons) = 5,544,695 number of mapped bases = 16,035,921,615 bp number of sequenced bases = 16,031,713,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,032,270 duplication rate = 7.4% >>>>>>> Insert size mean insert size = 166,008.2517 std insert size = 4,184,259.9032 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.1658 >>>>>>> ACTG content number of A's = 4,680,509,987 bp (29.2%) number of C's = 3,271,306,039 bp (20.41%) number of T's = 4,815,877,413 bp (30.04%) number of G's = 3,263,322,165 bp (20.36%) number of N's = 697,568 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0174 number of mismatches = 273,878,224 number of insertions = 2,331,686 mapped reads with insertion percentage = 1.2% number of deletions = 1,993,865 mapped reads with deletion percentage = 1.02% homopolymer indels = 36.78% >>>>>>> Coverage mean coverageData = 5.1801X std coverageData = 69.3575X There is a 87.94% of reference with a coverageData >= 1X There is a 80.79% of reference with a coverageData >= 2X There is a 70.89% of reference with a coverageData >= 3X There is a 59.69% of reference with a coverageData >= 4X There is a 48.4% of reference with a coverageData >= 5X There is a 37.99% of reference with a coverageData >= 6X There is a 28.99% of reference with a coverageData >= 7X There is a 21.6% of reference with a coverageData >= 8X There is a 15.78% of reference with a coverageData >= 9X There is a 11.34% of reference with a coverageData >= 10X There is a 8.05% of reference with a coverageData >= 11X There is a 5.67% of reference with a coverageData >= 12X There is a 3.97% of reference with a coverageData >= 13X There is a 2.79% of reference with a coverageData >= 14X There is a 1.96% of reference with a coverageData >= 15X There is a 1.39% of reference with a coverageData >= 16X There is a 1.01% of reference with a coverageData >= 17X There is a 0.74% of reference with a coverageData >= 18X There is a 0.56% of reference with a coverageData >= 19X There is a 0.43% of reference with a coverageData >= 20X There is a 0.35% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1477172911 5.926456291557243 176.6295307040176 chr2 243199373 1396123341 5.7406535377868755 101.02034162134247 chr3 198022430 1120766550 5.65979596351787 11.141405033408232 chr4 191154276 981379875 5.133967680639276 28.446973579800257 chr5 180915260 789628904 4.364634050217765 6.78533707834746 chr6 171115067 808100657 4.722556997274822 21.872208688431822 chr7 159138663 911740788 5.729222370053467 46.392303890683046 chr8 146364022 839859207 5.738153376244334 61.201614172731404 chr9 141213431 765934978 5.423952754182427 51.97240109528928 chr10 135534747 768858055 5.672774487858822 110.2468680134976 chr11 135006516 724503656 5.3664347282319325 33.10230727683472 chr12 133851895 599617750 4.479710578621244 6.154753859353765 chr13 115169878 507350466 4.405235768331716 4.200256810564142 chr14 107349540 353369698 3.291767230674673 29.191463842320406 chr15 102531392 414639585 4.044025706780612 5.19260329754165 chr16 90354753 550188618 6.089205047132385 58.543775243881086 chr17 81195210 307412655 3.78609347768175 16.902159720978567 chr18 78077248 623905889 7.990879609383773 64.29798912021278 chr19 59128983 304405014 5.1481523705557395 77.28444679087886 chr20 63025520 293085126 4.650261132315926 13.684019650057827 chr21 48129895 228114938 4.739568577907764 20.68225072826086 chr22 51304566 160259300 3.12368493673643 4.851837743797564 chrMT 16571 3183684 192.1238307887273 40.828487650826595 chrX 155270560 1057032786 6.807683220824347 22.32328014962201 chrY 59373566 49287184 0.8301199897611001 34.634179862310226