BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153317.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 = 187,284,870 number of mapped reads = 184,215,667 (98.36%) number of supplementary alignments = 1,114,244 (0.59%) number of secondary alignments = 0 number of mapped bases = 18,148,536,383 bp number of sequenced bases = 18,146,358,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,178,893 duplication rate = 70.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.5104 >>>>>>> ACTG content number of A's = 4,005,598,466 bp (22.07%) number of C's = 5,077,151,578 bp (27.98%) number of T's = 4,019,879,177 bp (22.15%) number of G's = 5,038,406,983 bp (27.77%) number of N's = 5,322,416 bp (0.03%) GC percentage = 55.74% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 76,076,072 number of insertions = 687,154 mapped reads with insertion percentage = 0.37% number of deletions = 794,037 mapped reads with deletion percentage = 0.42% homopolymer indels = 38.79% >>>>>>> Coverage mean coverageData = 5.8625X std coverageData = 75.2194X There is a 9.67% of reference with a coverageData >= 1X There is a 7.44% of reference with a coverageData >= 2X There is a 5.94% of reference with a coverageData >= 3X There is a 5.34% of reference with a coverageData >= 4X There is a 4.82% of reference with a coverageData >= 5X There is a 4.54% of reference with a coverageData >= 6X There is a 4.28% of reference with a coverageData >= 7X There is a 4.1% of reference with a coverageData >= 8X There is a 3.94% of reference with a coverageData >= 9X There is a 3.81% of reference with a coverageData >= 10X There is a 3.69% of reference with a coverageData >= 11X There is a 3.59% of reference with a coverageData >= 12X There is a 3.5% of reference with a coverageData >= 13X There is a 3.42% of reference with a coverageData >= 14X There is a 3.34% of reference with a coverageData >= 15X There is a 3.26% of reference with a coverageData >= 16X There is a 3.2% of reference with a coverageData >= 17X There is a 3.13% of reference with a coverageData >= 18X There is a 3.07% of reference with a coverageData >= 19X There is a 3.02% of reference with a coverageData >= 20X There is a 2.96% of reference with a coverageData >= 21X There is a 2.91% of reference with a coverageData >= 22X There is a 2.87% of reference with a coverageData >= 23X There is a 2.82% of reference with a coverageData >= 24X There is a 2.77% of reference with a coverageData >= 25X There is a 2.73% of reference with a coverageData >= 26X There is a 2.69% of reference with a coverageData >= 27X There is a 2.65% of reference with a coverageData >= 28X There is a 2.61% of reference with a coverageData >= 29X There is a 2.58% of reference with a coverageData >= 30X There is a 2.54% of reference with a coverageData >= 31X There is a 2.51% of reference with a coverageData >= 32X There is a 2.47% of reference with a coverageData >= 33X There is a 2.44% of reference with a coverageData >= 34X There is a 2.41% of reference with a coverageData >= 35X There is a 2.38% of reference with a coverageData >= 36X There is a 2.35% of reference with a coverageData >= 37X There is a 2.32% of reference with a coverageData >= 38X There is a 2.3% of reference with a coverageData >= 39X There is a 2.27% of reference with a coverageData >= 40X There is a 2.24% of reference with a coverageData >= 41X There is a 2.22% of reference with a coverageData >= 42X There is a 2.19% of reference with a coverageData >= 43X There is a 2.17% of reference with a coverageData >= 44X There is a 2.14% of reference with a coverageData >= 45X There is a 2.12% of reference with a coverageData >= 46X There is a 2.1% of reference with a coverageData >= 47X There is a 2.07% of reference with a coverageData >= 48X There is a 2.05% of reference with a coverageData >= 49X There is a 2.03% of reference with a coverageData >= 50X There is a 2.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1945404823 7.805014949190437 77.25068002780884 chr2 243199373 818687086 3.3663207100455805 37.55419651588354 chr3 198022430 812104992 4.101075782172757 44.048553322245986 chr4 191154276 467342915 2.444846773922023 48.272269096168195 chr5 180915260 968172036 5.351522232010722 119.73408160141736 chr6 171115067 400345102 2.339625078135288 27.396589325534848 chr7 159138663 928693472 5.835750121892127 96.88801471871254 chr8 146364022 859214232 5.870392329065677 102.26576158068718 chr9 141213431 445466543 3.154562139347779 31.525530210243208 chr10 135534747 612994355 4.522783777358584 48.2200839291268 chr11 135006516 1069361024 7.920810459252204 68.03218813952331 chr12 133851895 881307769 6.5842009110143715 63.69387547143752 chr13 115169878 98307731 0.8535889132399707 14.074536817409514 chr14 107349540 384442835 3.581224800776976 37.78036799981622 chr15 102531392 1024148606 9.988634563744146 104.56722820202488 chr16 90354753 975783088 10.799466055759126 91.34481124910761 chr17 81195210 1391680076 17.1399282790204 121.75470468901044 chr18 78077248 119402324 1.5292844850269314 22.079784721432567 chr19 59128983 1720299517 29.094014977392728 151.34165215468323 chr20 63025520 600709572 9.531211674255127 81.34442350526544 chr21 48129895 287982440 5.9834420997594115 179.97297234211032 chr22 51304566 590558967 11.510846169130444 91.7497458062676 chrMT 16571 6223 0.3755355741958844 0.8897254864554629 chrX 155270560 732361264 4.71667819063704 48.020992421915786 chrY 59373566 13759391 0.23174270853126794 10.94179184156617