BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006398.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 = 4,384,526 number of mapped reads = 3,728,825 (85.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,876,643 number of mapped paired reads (second in pair) = 1,852,182 number of mapped paired reads (both in pair) = 3,435,374 number of mapped paired reads (singletons) = 293,451 number of mapped bases = 144,294,370 bp number of sequenced bases = 144,276,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,883 duplication rate = 2.15% >>>>>>> Insert size mean insert size = 83,327.6236 std insert size = 2,790,973.0916 median insert size = 125 >>>>>>> Mapping quality mean mapping quality = 47.779 >>>>>>> ACTG content number of A's = 39,331,661 bp (27.26%) number of C's = 31,808,478 bp (22.05%) number of T's = 40,155,193 bp (27.83%) number of G's = 32,974,653 bp (22.86%) number of N's = 6,341 bp (0%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 441,770 number of insertions = 4,028 mapped reads with insertion percentage = 0.11% number of deletions = 13,521 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.13% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.2944X There is a 4.03% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 12038318 0.04829804616615178 0.35709276144469804 chr2 243199373 12154087 0.04997581552153097 0.2873588998233698 chr3 198022430 9381732 0.04737711783458066 0.24319814851533333 chr4 191154276 9039490 0.04728897615662021 0.2622580583856824 chr5 180915260 8590574 0.04748396569753154 0.24448799091464762 chr6 171115067 7953933 0.04648294939451474 0.25651416966318535 chr7 159138663 7544232 0.04740665692283716 0.3284324174860811 chr8 146364022 7242423 0.04948226279269642 0.5302400186056628 chr9 141213431 5943949 0.04209195228745628 0.2519945900201383 chr10 135534747 7074942 0.05220020811342201 0.30186608128944975 chr11 135006516 6932992 0.05135301765731071 0.28410541245707016 chr12 133851895 6395784 0.0477825435344042 0.2459356030398137 chr13 115169878 4420842 0.03838540143282951 0.21964653805763487 chr14 107349540 4303103 0.04008496915776258 0.2888845730727338 chr15 102531392 4330516 0.042236001243404556 0.23065021518298345 chr16 90354753 4434555 0.049079377152411674 0.27248416456721314 chr17 81195210 4202278 0.05175524516778761 0.2648408394554509 chr18 78077248 3672303 0.0470342269235719 0.3587779764341916 chr19 59128983 3074230 0.05199193092835708 0.3058964351359365 chr20 63025520 3318474 0.05265286188832714 0.26579270589047743 chr21 48129895 1915465 0.039797822122819924 0.2542530372705068 chr22 51304566 1904673 0.03712482432850129 0.2264655205766249 chrMT 16571 4188 0.25273067406915695 0.5912872895652522 chrX 155270560 8055395 0.05187973174051797 0.2671134536046836 chrY 59373566 365892 0.006162540414028694 0.1551559668618464