BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618609.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 33,431,120 number of mapped reads = 32,564,207 (97.41%) number of supplementary alignments = 39,088 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,421,967 number of mapped paired reads (second in pair) = 16,142,240 number of mapped paired reads (both in pair) = 32,126,686 number of mapped paired reads (singletons) = 437,521 number of mapped bases = 3,138,642,451 bp number of sequenced bases = 3,136,682,743 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,523,214 duplication rate = 12.65% >>>>>>> Insert size mean insert size = 24,815.7372 std insert size = 1,573,958.7126 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 54.0729 >>>>>>> ACTG content number of A's = 840,754,912 bp (26.8%) number of C's = 710,069,134 bp (22.64%) number of T's = 843,735,694 bp (26.9%) number of G's = 741,874,389 bp (23.65%) number of N's = 248,614 bp (0.01%) GC percentage = 46.29% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 35,884,684 number of insertions = 529,065 mapped reads with insertion percentage = 1.6% number of deletions = 1,429,781 mapped reads with deletion percentage = 4.29% homopolymer indels = 52.78% >>>>>>> Coverage mean coverageData = 1.0139X std coverageData = 4.2016X There is a 22.2% of reference with a coverageData >= 1X There is a 14.31% of reference with a coverageData >= 2X There is a 10.13% of reference with a coverageData >= 3X There is a 7.66% of reference with a coverageData >= 4X There is a 6.01% of reference with a coverageData >= 5X There is a 4.85% of reference with a coverageData >= 6X There is a 3.99% of reference with a coverageData >= 7X There is a 3.35% of reference with a coverageData >= 8X There is a 2.84% of reference with a coverageData >= 9X There is a 2.44% of reference with a coverageData >= 10X There is a 2.11% of reference with a coverageData >= 11X There is a 1.84% of reference with a coverageData >= 12X There is a 1.62% of reference with a coverageData >= 13X There is a 1.43% of reference with a coverageData >= 14X There is a 1.27% of reference with a coverageData >= 15X There is a 1.14% of reference with a coverageData >= 16X There is a 1.02% of reference with a coverageData >= 17X There is a 0.92% of reference with a coverageData >= 18X There is a 0.83% of reference with a coverageData >= 19X There is a 0.76% of reference with a coverageData >= 20X There is a 0.69% of reference with a coverageData >= 21X There is a 0.63% of reference with a coverageData >= 22X There is a 0.57% of reference with a coverageData >= 23X There is a 0.53% of reference with a coverageData >= 24X There is a 0.48% of reference with a coverageData >= 25X There is a 0.45% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.38% of reference with a coverageData >= 28X There is a 0.35% of reference with a coverageData >= 29X There is a 0.33% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 290759445 1.1665344857856943 5.12445219204717 chr2 243199373 249706903 1.0267580048407443 4.292137547280153 chr3 198022430 191429916 0.9667082461315115 3.56065416267953 chr4 191154276 138835122 0.726298803799712 3.307076606819288 chr5 180915260 165283588 0.9135967192596136 3.493832467863142 chr6 171115067 164092728 0.9589613052601615 3.7605642825988115 chr7 159138663 156217771 0.9816456168165746 3.699973894173024 chr8 146364022 148010855 1.011251624391683 3.7353648673357087 chr9 141213431 139456181 0.9875560703570753 4.515356004551807 chr10 135534747 158866885 1.1721487553298786 4.299068992963664 chr11 135006516 165303782 1.2244133609077061 4.759332111832604 chr12 133851895 138562186 1.03519031986809 3.885658056394872 chr13 115169878 76320327 0.6626761122383059 2.7954034489951973 chr14 107349540 99295697 0.9249755238820772 3.8546699667477453 chr15 102531392 108056992 1.0538917876000358 4.082239229110228 chr16 90354753 119482638 1.3223724710973424 5.9323859332766125 chr17 81195210 116719287 1.4375144420465198 5.231998769881655 chr18 78077248 78528980 1.005785705971604 4.454359054137855 chr19 59128983 79382045 1.3425234288233912 5.30922735924259 chr20 63025520 94921473 1.506079965702782 5.0998870152570515 chr21 48129895 39467912 0.8200290484739267 5.9319972492491875 chr22 51304566 64332444 1.2539321353970716 5.09604890671166 chrMT 16571 43070 2.5991189427312777 3.1317838855730327 chrX 155270560 151646990 0.9766628651303891 3.4903142642183593 chrY 59373566 3919234 0.0660097458185348 1.7332393457639454