BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506017.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,160,001 number of mapped reads = 4,443,933 (72.14%) number of supplementary alignments = 254 (0%) number of secondary alignments = 0 number of mapped bases = 206,730,993 bp number of sequenced bases = 206,688,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 219,523 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1723 >>>>>>> ACTG content number of A's = 60,830,411 bp (29.43%) number of C's = 42,425,314 bp (20.53%) number of T's = 59,877,291 bp (28.97%) number of G's = 42,910,766 bp (20.76%) number of N's = 645,217 bp (0.31%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,614,718 number of insertions = 8,986 mapped reads with insertion percentage = 0.2% number of deletions = 30,340 mapped reads with deletion percentage = 0.68% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.0668X std coverageData = 0.6102X There is a 5.36% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.19% 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 20298809 0.08143935175993001 1.1955411747082627 chr2 243199373 12402097 0.05099559611117912 0.4322148525713714 chr3 198022430 12857364 0.06492882649707915 0.3064397902749272 chr4 191154276 8944846 0.04679385775288647 0.2728400735998022 chr5 180915260 14942085 0.0825916232826352 0.34939245992721396 chr6 171115067 14032211 0.08200453207314584 0.43530270141221167 chr7 159138663 13254810 0.08329094734194166 1.173063279336308 chr8 146364022 11887930 0.08122166798613938 0.699683809594678 chr9 141213431 9611739 0.06806533154767694 0.42852655023063846 chr10 135534747 6538380 0.048241356144635 0.5505785591319179 chr11 135006516 10819283 0.08013896899613349 0.49548689702763543 chr12 133851895 5908751 0.04414394730832911 0.28030406936356683 chr13 115169878 6545483 0.05683328934324303 0.28126847645559083 chr14 107349540 7539888 0.07023679840640211 0.932316946415603 chr15 102531392 6576040 0.06413684503571355 0.30023419161130105 chr16 90354753 6239566 0.06905631184670495 0.35347679947151317 chr17 81195210 3265304 0.04021547576513442 0.2696183909472816 chr18 78077248 6336905 0.08116199228743308 0.7414451309890221 chr19 59128983 5027042 0.08501823885589238 0.8712144553084675 chr20 63025520 4826805 0.0765849294063738 0.34551487770797235 chr21 48129895 2989370 0.06211046169953207 0.3361385255588122 chr22 51304566 1513125 0.029492988986594294 0.20261597110011784 chrMT 16571 42805 2.5831271498400823 2.2881668214071493 chrX 155270560 13700156 0.0882340863586761 0.4208358805783797 chrY 59373566 630199 0.010614134242837966 0.1737948287507183