BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124914.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,587,714 number of mapped reads = 4,491,725 (97.91%) number of supplementary alignments = 22,439 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,250,752 number of mapped paired reads (second in pair) = 2,240,973 number of mapped paired reads (both in pair) = 4,469,684 number of mapped paired reads (singletons) = 22,041 number of mapped bases = 394,582,387 bp number of sequenced bases = 394,366,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 336,106 duplication rate = 4.52% >>>>>>> Insert size mean insert size = 42,398.6779 std insert size = 1,871,436.9092 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.793 >>>>>>> ACTG content number of A's = 111,039,966 bp (28.16%) number of C's = 74,819,048 bp (18.97%) number of T's = 116,997,754 bp (29.67%) number of G's = 91,497,546 bp (23.2%) number of N's = 11,741 bp (0%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 2,872,650 number of insertions = 58,112 mapped reads with insertion percentage = 1.25% number of deletions = 120,415 mapped reads with deletion percentage = 2.62% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.1275X std coverageData = 1.3794X There is a 9.19% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 32458379 0.13022386411627035 1.4778402671785626 chr2 243199373 36449064 0.14987318244443007 1.6397124566746324 chr3 198022430 26120208 0.13190529981881347 0.4645941486683783 chr4 191154276 25796432 0.13495084985700243 0.9610825782468722 chr5 180915260 18751994 0.10365070364987453 0.462000033013958 chr6 171115067 27871294 0.1628804201093525 2.8637118519460576 chr7 159138663 20942268 0.13159761182610916 1.1679134313091093 chr8 146364022 22482393 0.1536060070828062 0.6407721250909171 chr9 141213431 22376079 0.1584557420745623 1.6891139500636627 chr10 135534747 19092717 0.1408695365772144 2.679235109783656 chr11 135006516 15493688 0.11476252005495793 1.3338758690959227 chr12 133851895 17991021 0.1344099088025612 0.5209086387803972 chr13 115169878 9163720 0.07956698538831482 0.34343089825509804 chr14 107349540 8863550 0.0825671912520538 0.4397704260476835 chr15 102531392 14825943 0.14459906093930724 0.48876636291297537 chr16 90354753 13124429 0.14525443946485028 2.0760077864139177 chr17 81195210 8285739 0.10204714046555209 0.9990315739497274 chr18 78077248 8234121 0.10546120939098673 1.6512258207573116 chr19 59128983 4686471 0.07925844082249817 1.0236689841909397 chr20 63025520 11576927 0.18368633848637822 0.6065249239640009 chr21 48129895 5748366 0.11943441804724486 0.7097562344135695 chr22 51304566 6081097 0.11852935272856611 0.46102015120036116 chrMT 16571 201477 12.158409269205238 6.578540373171636 chrX 155270560 15875134 0.1022417514305352 0.6310104636742534 chrY 59373566 2089876 0.035198761684619044 1.6984473475274044