BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617650.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,922,801 (93.51%) number of supplementary alignments = 140,790 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,008,801 number of mapped paired reads (second in pair) = 14,914,000 number of mapped paired reads (both in pair) = 29,292,516 number of mapped paired reads (singletons) = 630,285 number of mapped bases = 2,900,137,491 bp number of sequenced bases = 2,898,388,831 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,761,182 duplication rate = 10.55% >>>>>>> Insert size mean insert size = 32,428.5586 std insert size = 1,638,816.0914 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.6159 >>>>>>> ACTG content number of A's = 864,723,437 bp (29.83%) number of C's = 577,354,765 bp (19.92%) number of T's = 862,115,426 bp (29.74%) number of G's = 592,295,574 bp (20.44%) number of N's = 1,899,629 bp (0.07%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0158 number of mismatches = 44,877,054 number of insertions = 451,975 mapped reads with insertion percentage = 1.48% number of deletions = 1,059,204 mapped reads with deletion percentage = 3.47% homopolymer indels = 47.66% >>>>>>> Coverage mean coverageData = 0.9368X std coverageData = 10.5236X There is a 33.11% of reference with a coverageData >= 1X There is a 19.11% of reference with a coverageData >= 2X There is a 11.63% of reference with a coverageData >= 3X There is a 7.4% of reference with a coverageData >= 4X There is a 4.85% of reference with a coverageData >= 5X There is a 3.28% of reference with a coverageData >= 6X There is a 2.26% of reference with a coverageData >= 7X There is a 1.6% of reference with a coverageData >= 8X There is a 1.16% of reference with a coverageData >= 9X There is a 0.86% of reference with a coverageData >= 10X There is a 0.64% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177708820 0.7129724262552589 10.203836501672875 chr2 243199373 299730177 1.2324463394072978 11.988783752938415 chr3 198022430 242997521 1.2271211953110563 2.4521573610017944 chr4 191154276 162666510 0.8509697685235145 8.242493432165862 chr5 180915260 192087834 1.061755840828463 2.3033793553118596 chr6 171115067 140911646 0.8234905813408003 5.712099606719659 chr7 159138663 226701239 1.4245516125770141 13.165798907182396 chr8 146364022 129130492 0.882255695323814 4.080657079732624 chr9 141213431 119200626 0.8441167752662281 20.25248235862577 chr10 135534747 122839248 0.9063303006719008 21.530160339629617 chr11 135006516 159216991 1.1793281962775781 11.890480864376702 chr12 133851895 123793934 0.9248575375044186 2.117309794586998 chr13 115169878 124791947 1.0835467499583529 2.258166268942711 chr14 107349540 82700053 0.7703810654428515 2.42871696125848 chr15 102531392 61881793 0.6035399675447691 1.561975204967275 chr16 90354753 80487636 0.8907958167956035 16.892562222986196 chr17 81195210 70982992 0.8742263490666506 12.522537426518118 chr18 78077248 53606623 0.6865844323816331 18.07573378635365 chr19 59128983 30537033 0.5164477968444003 6.046991837112652 chr20 63025520 78058058 1.2385150967417642 3.016631631934868 chr21 48129895 42238370 0.8775911520272379 4.359304113717584 chr22 51304566 18458234 0.35977760731861563 1.2428140265397698 chrMT 16571 3072673 185.42471788063483 128.55107995168058 chrX 155270560 144651969 0.9316123352681925 4.309266047078658 chrY 59373566 11685072 0.19680596580639945 17.22405992623138