BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504589.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 = 351,856,500 number of mapped reads = 336,815,366 (95.73%) number of supplementary alignments = 967,230 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 168,614,898 number of mapped paired reads (second in pair) = 168,200,468 number of mapped paired reads (both in pair) = 334,117,234 number of mapped paired reads (singletons) = 2,698,132 number of mapped bases = 32,358,012,165 bp number of sequenced bases = 32,347,611,311 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,611,268 duplication rate = 17.6% >>>>>>> Insert size mean insert size = 33,847.0129 std insert size = 1,744,286.5508 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.3728 >>>>>>> ACTG content number of A's = 9,190,938,049 bp (28.41%) number of C's = 6,937,659,860 bp (21.45%) number of T's = 9,098,664,279 bp (28.13%) number of G's = 7,109,566,283 bp (21.98%) number of N's = 10,782,840 bp (0.03%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 187,003,383 number of insertions = 3,279,145 mapped reads with insertion percentage = 0.94% number of deletions = 4,023,347 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.4% >>>>>>> Coverage mean coverageData = 10.4526X std coverageData = 92.1399X There is a 90.8% of reference with a coverageData >= 1X There is a 88.89% of reference with a coverageData >= 2X There is a 85.66% of reference with a coverageData >= 3X There is a 81.2% of reference with a coverageData >= 4X There is a 75.69% of reference with a coverageData >= 5X There is a 69.44% of reference with a coverageData >= 6X There is a 62.79% of reference with a coverageData >= 7X There is a 56.05% of reference with a coverageData >= 8X There is a 49.46% of reference with a coverageData >= 9X There is a 43.21% of reference with a coverageData >= 10X There is a 37.44% of reference with a coverageData >= 11X There is a 32.22% of reference with a coverageData >= 12X There is a 27.58% of reference with a coverageData >= 13X There is a 23.51% of reference with a coverageData >= 14X There is a 19.99% of reference with a coverageData >= 15X There is a 16.97% of reference with a coverageData >= 16X There is a 14.4% of reference with a coverageData >= 17X There is a 12.24% of reference with a coverageData >= 18X There is a 10.42% of reference with a coverageData >= 19X There is a 8.9% of reference with a coverageData >= 20X There is a 7.64% of reference with a coverageData >= 21X There is a 6.58% of reference with a coverageData >= 22X There is a 5.71% of reference with a coverageData >= 23X There is a 4.98% of reference with a coverageData >= 24X There is a 4.37% of reference with a coverageData >= 25X There is a 3.86% of reference with a coverageData >= 26X There is a 3.43% of reference with a coverageData >= 27X There is a 3.07% of reference with a coverageData >= 28X There is a 2.77% of reference with a coverageData >= 29X There is a 2.51% of reference with a coverageData >= 30X There is a 2.29% of reference with a coverageData >= 31X There is a 2.1% of reference with a coverageData >= 32X There is a 1.94% of reference with a coverageData >= 33X There is a 1.8% of reference with a coverageData >= 34X There is a 1.67% of reference with a coverageData >= 35X There is a 1.56% of reference with a coverageData >= 36X There is a 1.46% of reference with a coverageData >= 37X There is a 1.38% of reference with a coverageData >= 38X There is a 1.3% of reference with a coverageData >= 39X There is a 1.23% of reference with a coverageData >= 40X There is a 1.16% of reference with a coverageData >= 41X There is a 1.11% of reference with a coverageData >= 42X There is a 1.05% of reference with a coverageData >= 43X There is a 1% of reference with a coverageData >= 44X There is a 0.96% of reference with a coverageData >= 45X There is a 0.92% of reference with a coverageData >= 46X There is a 0.88% of reference with a coverageData >= 47X There is a 0.84% of reference with a coverageData >= 48X There is a 0.81% of reference with a coverageData >= 49X There is a 0.78% of reference with a coverageData >= 50X There is a 0.75% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3009141232 12.072753198877686 167.25815810131147 chr2 243199373 2285408150 9.397261686196863 55.452197773996886 chr3 198022430 1914574952 9.668475192431483 16.054793205866215 chr4 191154276 1834971154 9.599425094733428 110.17009563801851 chr5 180915260 1527994658 8.445913617237153 10.00206651517923 chr6 171115067 1516115777 8.860212040825136 21.692305784819197 chr7 159138663 2729632642 17.15254225806836 132.52983383282807 chr8 146364022 2844952026 19.437509212475728 64.74595149439392 chr9 141213431 1166941149 8.263669685923855 58.359397947517486 chr10 135534747 1576291456 11.630164890483767 249.98070952255483 chr11 135006516 1389319416 10.290758232735966 37.26753675605321 chr12 133851895 1208937390 9.031903433268539 8.367926324490433 chr13 115169878 785404495 6.819530493902234 6.216622875740127 chr14 107349540 1049620282 9.777594594257227 9.200753344855531 chr15 102531392 844344426 8.2349845206432 7.0174097211132445 chr16 90354753 898985234 9.94950685106737 71.21619457259096 chr17 81195210 1002500489 12.346793474639698 43.459557124406814 chr18 78077248 551616953 7.065015316625914 91.38644949384327 chr19 59128983 646795529 10.938722369028401 86.51619212677959 chr20 63025520 1360012578 21.578760127643534 28.12573285478075 chr21 48129895 388055948 8.062680128431612 38.72464494344718 chr22 51304566 436265979 8.503453259891137 9.143471890439548 chrMT 16571 115959182 6997.717820288456 1483.2243874730602 chrX 155270560 1149832766 7.4053495137777565 18.127577689404358 chrY 59373566 124338302 2.0941693480226538 112.24025426958411