BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777308.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 = 364,320,754 number of mapped reads = 344,125,158 (94.46%) number of supplementary alignments = 10,719,492 (2.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 173,137,169 number of mapped paired reads (second in pair) = 170,987,989 number of mapped paired reads (both in pair) = 338,319,248 number of mapped paired reads (singletons) = 5,805,910 number of mapped bases = 32,763,213,918 bp number of sequenced bases = 32,728,461,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,225,794 duplication rate = 22.84% >>>>>>> Insert size mean insert size = 146,246.5893 std insert size = 3,738,075.7618 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.4768 >>>>>>> ACTG content number of A's = 9,453,504,576 bp (28.88%) number of C's = 6,954,695,447 bp (21.25%) number of T's = 9,248,363,555 bp (28.26%) number of G's = 7,070,982,551 bp (21.6%) number of N's = 915,506 bp (0%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 302,672,865 number of insertions = 11,791,267 mapped reads with insertion percentage = 3.14% number of deletions = 10,756,334 mapped reads with deletion percentage = 2.82% homopolymer indels = 29.02% >>>>>>> Coverage mean coverageData = 10.5835X std coverageData = 386.1113X There is a 61.2% of reference with a coverageData >= 1X There is a 52.32% of reference with a coverageData >= 2X There is a 45.02% of reference with a coverageData >= 3X There is a 39.77% of reference with a coverageData >= 4X There is a 35.5% of reference with a coverageData >= 5X There is a 32% of reference with a coverageData >= 6X There is a 29.05% of reference with a coverageData >= 7X There is a 26.53% of reference with a coverageData >= 8X There is a 24.35% of reference with a coverageData >= 9X There is a 22.44% of reference with a coverageData >= 10X There is a 20.77% of reference with a coverageData >= 11X There is a 19.28% of reference with a coverageData >= 12X There is a 17.95% of reference with a coverageData >= 13X There is a 16.76% of reference with a coverageData >= 14X There is a 15.68% of reference with a coverageData >= 15X There is a 14.7% of reference with a coverageData >= 16X There is a 13.82% of reference with a coverageData >= 17X There is a 13.01% of reference with a coverageData >= 18X There is a 12.27% of reference with a coverageData >= 19X There is a 11.59% of reference with a coverageData >= 20X There is a 10.96% of reference with a coverageData >= 21X There is a 10.39% of reference with a coverageData >= 22X There is a 9.85% of reference with a coverageData >= 23X There is a 9.36% of reference with a coverageData >= 24X There is a 8.9% of reference with a coverageData >= 25X There is a 8.47% of reference with a coverageData >= 26X There is a 8.07% of reference with a coverageData >= 27X There is a 7.7% of reference with a coverageData >= 28X There is a 7.35% of reference with a coverageData >= 29X There is a 7.02% of reference with a coverageData >= 30X There is a 6.71% of reference with a coverageData >= 31X There is a 6.42% of reference with a coverageData >= 32X There is a 6.15% of reference with a coverageData >= 33X There is a 5.9% of reference with a coverageData >= 34X There is a 5.65% of reference with a coverageData >= 35X There is a 5.43% of reference with a coverageData >= 36X There is a 5.21% of reference with a coverageData >= 37X There is a 5.01% of reference with a coverageData >= 38X There is a 4.81% of reference with a coverageData >= 39X There is a 4.63% of reference with a coverageData >= 40X There is a 4.46% of reference with a coverageData >= 41X There is a 4.29% of reference with a coverageData >= 42X There is a 4.14% of reference with a coverageData >= 43X There is a 3.99% of reference with a coverageData >= 44X There is a 3.85% of reference with a coverageData >= 45X There is a 3.71% of reference with a coverageData >= 46X There is a 3.58% of reference with a coverageData >= 47X There is a 3.46% of reference with a coverageData >= 48X There is a 3.34% of reference with a coverageData >= 49X There is a 3.23% of reference with a coverageData >= 50X There is a 3.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2522587245 10.12068589790996 175.31167868208507 chr2 243199373 2846021972 11.70242314728336 298.94053271445324 chr3 198022430 1844473636 9.31446824483469 179.411635463907 chr4 191154276 1979310489 10.354518509436849 285.6877842790922 chr5 180915260 1646654251 9.101798549221332 78.83306135179826 chr6 171115067 1636884822 9.565988844220247 182.9405170955988 chr7 159138663 1560880668 9.808305779218466 95.20866935805736 chr8 146364022 1415403550 9.670433557776924 60.036299005525244 chr9 141213431 1361595551 9.64211082018112 163.1319130583833 chr10 135534747 2688943835 19.839516393534126 1490.6062346006483 chr11 135006516 1379437351 10.2175612842272 73.19406725212399 chr12 133851895 1258589648 9.402852667868467 40.35949279839577 chr13 115169878 894065054 7.763011210274964 131.84078781186292 chr14 107349540 1197582606 11.155917445011875 478.10954840036203 chr15 102531392 868014045 8.465836931190792 125.58100181192607 chr16 90354753 1797809507 19.897232268456314 571.8297424660736 chr17 81195210 832696288 10.25548536668604 61.530623604815155 chr18 78077248 812913926 10.411662127230715 132.2033390935942 chr19 59128983 624902685 10.568466651963217 125.97904200746952 chr20 63025520 675689615 10.72088917314764 86.12261423322569 chr21 48129895 468426259 9.73254271591492 173.15874755426898 chr22 51304566 437826616 8.53387232629548 78.76466085479062 chrMT 16571 645436491 38949.76108864885 6213.611252070703 chrX 155270560 821211236 5.288904966917102 111.47617068694701 chrY 59373566 545856572 9.19359588406733 296.5008731710539