BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006000.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 14,309,920 number of mapped reads = 11,908,794 (83.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,025,098 number of mapped paired reads (second in pair) = 5,883,696 number of mapped paired reads (both in pair) = 10,867,376 number of mapped paired reads (singletons) = 1,041,418 number of mapped bases = 460,217,441 bp number of sequenced bases = 460,166,579 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 691,282 duplication rate = 4.95% >>>>>>> Insert size mean insert size = 60,950.3688 std insert size = 2,382,612.921 median insert size = 85 >>>>>>> Mapping quality mean mapping quality = 46.5222 >>>>>>> ACTG content number of A's = 130,475,144 bp (28.35%) number of C's = 98,536,509 bp (21.41%) number of T's = 131,152,247 bp (28.5%) number of G's = 99,861,482 bp (21.7%) number of N's = 141,197 bp (0.03%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 2,283,899 number of insertions = 14,093 mapped reads with insertion percentage = 0.12% number of deletions = 39,607 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.9% >>>>>>> Coverage mean coverageData = 0.1487X std coverageData = 0.9955X There is a 9.25% of reference with a coverageData >= 1X There is a 3.38% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 37986989 0.15240479180190286 1.3706008959599945 chr2 243199373 39715835 0.16330566362109825 0.7321090063467797 chr3 198022430 32216315 0.16269023160659124 0.5873062472950293 chr4 191154276 30348307 0.15876342206438532 0.611795895929717 chr5 180915260 28431884 0.15715580874714494 0.5773068110295896 chr6 171115067 26823199 0.15675533119476848 0.6798175619943544 chr7 159138663 25112513 0.1578027144792589 1.0334437367449505 chr8 146364022 23891589 0.16323402892003064 3.04734281129335 chr9 141213431 19001611 0.1345595165094459 0.6327528750297132 chr10 135534747 21039515 0.15523336609762514 0.7030509614292438 chr11 135006516 20735470 0.15358866086137649 0.6704960936731593 chr12 133851895 20634307 0.1541577502507529 0.5781837787849882 chr13 115169878 14979373 0.1300632879024149 0.5242619453104699 chr14 107349540 13840778 0.12893187991303923 0.5591853865049995 chr15 102531392 13028840 0.12707171672847278 0.5218465881121318 chr16 90354753 12551151 0.13890969299644923 0.5804538978827193 chr17 81195210 11605501 0.1429333208202799 0.580445359477545 chr18 78077248 12027653 0.15404811655246864 0.9633330749148438 chr19 59128983 8498756 0.14373249071440988 1.1858883140961758 chr20 63025520 9495906 0.15066763431701952 0.5949108175678776 chr21 48129895 5805762 0.12062694090647819 0.5548377180970362 chr22 51304566 5043369 0.0983025370490416 0.5284365324014789 chrMT 16571 51338 3.098062880936576 2.700673269374476 chrX 155270560 26251599 0.1690700349119627 0.6510053241551585 chrY 59373566 1099881 0.01852475898112638 0.32087753724612544