BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975290.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 3,327,746 number of mapped reads = 3,294,312 (99%) number of supplementary alignments = 17,433 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,646,759 number of mapped paired reads (second in pair) = 1,647,553 number of mapped paired reads (both in pair) = 3,283,614 number of mapped paired reads (singletons) = 10,698 number of mapped bases = 301,325,644 bp number of sequenced bases = 301,161,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 153,695 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 48,558.9704 std insert size = 2,101,040.4555 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.8591 >>>>>>> ACTG content number of A's = 86,866,069 bp (28.84%) number of C's = 57,932,604 bp (19.24%) number of T's = 91,341,624 bp (30.33%) number of G's = 65,014,336 bp (21.59%) number of N's = 6,634 bp (0%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 2,451,470 number of insertions = 49,440 mapped reads with insertion percentage = 1.47% number of deletions = 100,419 mapped reads with deletion percentage = 2.99% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.0973X std coverageData = 1.0386X There is a 6.98% of reference with a coverageData >= 1X There is a 1.84% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 27910274 0.11197674809403986 1.0798128449775835 chr2 243199373 26132793 0.10745419561587438 1.0732955168228937 chr3 198022430 16356902 0.08260125885739307 0.3874703947070271 chr4 191154276 20336679 0.1063888259554288 0.6580440123039119 chr5 180915260 19126508 0.10572081094762266 0.4113136995564761 chr6 171115067 21972641 0.12840856965564582 0.8699577101142655 chr7 159138663 17916688 0.11258538724810073 1.1735199169760324 chr8 146364022 15801970 0.10796348572602084 0.5185552515785445 chr9 141213431 13222114 0.09363212766921583 1.410399973777499 chr10 135534747 16827815 0.12415867792190588 3.007890736722374 chr11 135006516 11319695 0.08384554564758934 0.9393161200816418 chr12 133851895 13647058 0.10195640487570236 0.40548541312762804 chr13 115169878 10657745 0.09253934435877409 0.38045598359755717 chr14 107349540 9027392 0.08409343905898432 0.4053515642990461 chr15 102531392 8670617 0.08456548605133538 0.3672247757718805 chr16 90354753 9977207 0.11042260278216907 1.4788044509960754 chr17 81195210 6239640 0.07684739038177252 0.7915637902449382 chr18 78077248 8766740 0.11228290218425731 1.4772500738319136 chr19 59128983 3905168 0.06604490390101923 0.6575973920726718 chr20 63025520 6369952 0.10106940807469736 0.4362536984238308 chr21 48129895 3794634 0.0788415183536137 0.4800734804552477 chr22 51304566 2747641 0.05355548665980334 0.29311812987056063 chrMT 16571 261688 15.791925653249653 25.19123865600035 chrX 155270560 9707636 0.0625207766366013 0.4518451739686849 chrY 59373566 628447 0.010584626161750163 0.5999382240398061