BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006024.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 = 8,669,660 number of mapped reads = 5,887,474 (67.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,982,558 number of mapped paired reads (second in pair) = 2,904,916 number of mapped paired reads (both in pair) = 5,077,518 number of mapped paired reads (singletons) = 809,956 number of mapped bases = 227,339,031 bp number of sequenced bases = 227,314,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,416 duplication rate = 1.93% >>>>>>> Insert size mean insert size = 73,457.8246 std insert size = 2,622,854.9587 median insert size = 102 >>>>>>> Mapping quality mean mapping quality = 46.9871 >>>>>>> ACTG content number of A's = 67,326,832 bp (29.62%) number of C's = 46,571,698 bp (20.49%) number of T's = 66,120,138 bp (29.09%) number of G's = 47,212,712 bp (20.77%) number of N's = 83,135 bp (0.04%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,672,365 number of insertions = 6,358 mapped reads with insertion percentage = 0.11% number of deletions = 19,231 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.69% >>>>>>> Coverage mean coverageData = 0.0734X std coverageData = 0.4237X There is a 5.93% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 18475725 0.07412509114671373 0.5884959319521812 chr2 243199373 19272379 0.07924518374477882 0.39849342113112457 chr3 198022430 15825826 0.07991936065020513 0.3339366268447124 chr4 191154276 15235832 0.07970437449173254 0.3688806103566654 chr5 180915260 14454281 0.07989531120813137 0.3334529008931061 chr6 171115067 13455921 0.07863668136248926 0.4061703231456678 chr7 159138663 12402389 0.07793448032173049 0.4610389169399713 chr8 146364022 11410984 0.0779630393048368 0.8487929145113993 chr9 141213431 9226688 0.06533860083039834 0.3418949073613189 chr10 135534747 10498911 0.07746287378246997 0.4556229307912126 chr11 135006516 10236284 0.07582066631509846 0.34839561097769084 chr12 133851895 10567886 0.07895208356967975 0.33254787722029755 chr13 115169878 7660782 0.06651723639057776 0.3038674730489691 chr14 107349540 6884378 0.06413048439704538 0.3151987477300307 chr15 102531392 6371390 0.06214087096369471 0.2940036285604881 chr16 90354753 6196016 0.06857432281398633 0.35268355554076913 chr17 81195210 5661569 0.06972786941495687 0.3175404843945712 chr18 78077248 6007488 0.07694287585546047 0.4885797269012523 chr19 59128983 4007133 0.06776935432831645 0.45335563643903576 chr20 63025520 4521700 0.0717439538777308 0.32933013444956355 chr21 48129895 2997076 0.062270570089546215 0.32220188935440747 chr22 51304566 2350557 0.04581574669201958 0.2530863065076789 chrMT 16571 6402 0.3863375776959749 0.794056413004972 chrX 155270560 13033427 0.0839401042927906 0.36431869700386404 chrY 59373566 578007 0.009735089854633288 0.21109178262404973