BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630491.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 267,169,308 number of mapped reads = 264,538,926 (99.02%) number of supplementary alignments = 596,538 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 133,304,043 number of mapped paired reads (second in pair) = 131,234,883 number of mapped paired reads (both in pair) = 262,323,530 number of mapped paired reads (singletons) = 2,215,396 number of mapped bases = 25,787,066,307 bp number of sequenced bases = 25,778,833,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,961,708 duplication rate = 12.27% >>>>>>> Insert size mean insert size = 45,192.2634 std insert size = 2,011,213.4559 median insert size = 392 >>>>>>> Mapping quality mean mapping quality = 53.5654 >>>>>>> ACTG content number of A's = 7,866,112,958 bp (30.51%) number of C's = 5,072,985,185 bp (19.68%) number of T's = 7,764,376,932 bp (30.12%) number of G's = 5,069,064,345 bp (19.66%) number of N's = 6,293,986 bp (0.02%) GC percentage = 39.34% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 269,868,669 number of insertions = 3,001,150 mapped reads with insertion percentage = 1.1% number of deletions = 3,791,741 mapped reads with deletion percentage = 1.39% homopolymer indels = 42.07% >>>>>>> Coverage mean coverageData = 8.33X std coverageData = 106.059X There is a 91.84% of reference with a coverageData >= 1X There is a 90.58% of reference with a coverageData >= 2X There is a 88.09% of reference with a coverageData >= 3X There is a 84.01% of reference with a coverageData >= 4X There is a 78.2% of reference with a coverageData >= 5X There is a 70.77% of reference with a coverageData >= 6X There is a 62.07% of reference with a coverageData >= 7X There is a 52.67% of reference with a coverageData >= 8X There is a 43.18% of reference with a coverageData >= 9X There is a 34.2% of reference with a coverageData >= 10X There is a 26.18% of reference with a coverageData >= 11X There is a 19.41% of reference with a coverageData >= 12X There is a 13.95% of reference with a coverageData >= 13X There is a 9.76% of reference with a coverageData >= 14X There is a 6.66% of reference with a coverageData >= 15X There is a 4.47% of reference with a coverageData >= 16X There is a 2.96% of reference with a coverageData >= 17X There is a 1.96% of reference with a coverageData >= 18X There is a 1.31% of reference with a coverageData >= 19X There is a 0.9% of reference with a coverageData >= 20X There is a 0.65% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.39% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2084341616 8.362432990688516 236.3068250016423 chr2 243199373 2286052570 9.39991144631775 68.26778880274743 chr3 198022430 1769929155 8.938023611769637 8.138664417991707 chr4 191154276 1855978475 9.709322301531984 75.985487583039 chr5 180915260 1622165291 8.966437054563556 6.955822964034708 chr6 171115067 1530666375 8.945246037276192 19.887246869887107 chr7 159138663 1419942248 8.922672977339266 69.82606347328637 chr8 146364022 1380718815 9.43345773184615 219.50583578682375 chr9 141213431 1121249978 7.9401086005763855 147.1341253361346 chr10 135534747 1348845598 9.952028006515555 166.62276366257535 chr11 135006516 1174284381 8.697982999576109 46.90285245924786 chr12 133851895 1147358909 8.571854055558944 9.687322764448627 chr13 115169878 876783904 7.612961993412895 5.173816704353276 chr14 107349540 775048193 7.219855744141987 9.924519605250826 chr15 102531392 695054719 6.778945505782268 5.568897110358375 chr16 90354753 760247354 8.414027251006928 68.94378630249957 chr17 81195210 641354120 7.898915711899754 54.89803460072366 chr18 78077248 756603839 9.690452191655115 147.2115461486043 chr19 59128983 434567626 7.34948588579648 118.45484256579547 chr20 63025520 496840161 7.883158457082147 17.385301979716125 chr21 48129895 365136291 7.586475952212237 25.14951760722341 chr22 51304566 263332171 5.132723878806421 21.614727054214633 chrMT 16571 4154977 250.73785528936094 37.90841456341419 chrX 155270560 721604249 4.647399024000428 17.939314245439377 chrY 59373566 254805292 4.291561197452752 68.22647179883825