BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504619.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 = 299,995,974 number of mapped reads = 283,676,668 (94.56%) number of supplementary alignments = 3,090,492 (1.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 142,392,541 number of mapped paired reads (second in pair) = 141,284,127 number of mapped paired reads (both in pair) = 279,093,806 number of mapped paired reads (singletons) = 4,582,862 number of mapped bases = 27,296,525,836 bp number of sequenced bases = 27,271,094,163 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,254,802 duplication rate = 18.17% >>>>>>> Insert size mean insert size = 115,540.8416 std insert size = 3,205,702.081 median insert size = 336 >>>>>>> Mapping quality mean mapping quality = 52.3134 >>>>>>> ACTG content number of A's = 7,273,602,269 bp (26.67%) number of C's = 6,312,022,780 bp (23.15%) number of T's = 7,348,824,311 bp (26.95%) number of G's = 6,332,474,387 bp (23.22%) number of N's = 4,170,416 bp (0.02%) GC percentage = 46.37% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 285,842,158 number of insertions = 8,313,098 mapped reads with insertion percentage = 2.71% number of deletions = 7,716,956 mapped reads with deletion percentage = 2.53% homopolymer indels = 34.65% >>>>>>> Coverage mean coverageData = 8.8176X std coverageData = 219.2619X There is a 83.1% of reference with a coverageData >= 1X There is a 74.25% of reference with a coverageData >= 2X There is a 65.86% of reference with a coverageData >= 3X There is a 58.42% of reference with a coverageData >= 4X There is a 51.86% of reference with a coverageData >= 5X There is a 46.1% of reference with a coverageData >= 6X There is a 41.03% of reference with a coverageData >= 7X There is a 36.55% of reference with a coverageData >= 8X There is a 32.57% of reference with a coverageData >= 9X There is a 29.03% of reference with a coverageData >= 10X There is a 25.87% of reference with a coverageData >= 11X There is a 23.06% of reference with a coverageData >= 12X There is a 20.54% of reference with a coverageData >= 13X There is a 18.3% of reference with a coverageData >= 14X There is a 16.3% of reference with a coverageData >= 15X There is a 14.52% of reference with a coverageData >= 16X There is a 12.94% of reference with a coverageData >= 17X There is a 11.53% of reference with a coverageData >= 18X There is a 10.28% of reference with a coverageData >= 19X There is a 9.17% of reference with a coverageData >= 20X There is a 8.18% of reference with a coverageData >= 21X There is a 7.31% of reference with a coverageData >= 22X There is a 6.53% of reference with a coverageData >= 23X There is a 5.84% of reference with a coverageData >= 24X There is a 5.23% of reference with a coverageData >= 25X There is a 4.7% of reference with a coverageData >= 26X There is a 4.22% of reference with a coverageData >= 27X There is a 3.8% of reference with a coverageData >= 28X There is a 3.43% of reference with a coverageData >= 29X There is a 3.1% of reference with a coverageData >= 30X There is a 2.8% of reference with a coverageData >= 31X There is a 2.54% of reference with a coverageData >= 32X There is a 2.31% of reference with a coverageData >= 33X There is a 2.11% of reference with a coverageData >= 34X There is a 1.93% of reference with a coverageData >= 35X There is a 1.77% of reference with a coverageData >= 36X There is a 1.63% of reference with a coverageData >= 37X There is a 1.5% of reference with a coverageData >= 38X There is a 1.38% of reference with a coverageData >= 39X There is a 1.28% of reference with a coverageData >= 40X There is a 1.19% of reference with a coverageData >= 41X There is a 1.11% of reference with a coverageData >= 42X There is a 1.04% of reference with a coverageData >= 43X There is a 0.97% of reference with a coverageData >= 44X There is a 0.91% of reference with a coverageData >= 45X There is a 0.86% of reference with a coverageData >= 46X There is a 0.81% of reference with a coverageData >= 47X There is a 0.77% of reference with a coverageData >= 48X There is a 0.73% of reference with a coverageData >= 49X There is a 0.69% of reference with a coverageData >= 50X There is a 0.66% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2103347378 8.438684604119803 62.24660197456605 chr2 243199373 2162895632 8.893508257523346 229.40533606584955 chr3 198022430 1448599307 7.315329414955669 19.861852828006096 chr4 191154276 2050834652 10.728688339673866 617.9494240421309 chr5 180915260 1413157593 7.811157516508005 32.346644535717 chr6 171115067 1162463528 6.793460963902144 30.085436433449118 chr7 159138663 1341666441 8.430801262921255 32.61475823558197 chr8 146364022 1275908136 8.717361811770928 153.80327397322515 chr9 141213431 997055359 7.060626966849917 65.49936600257739 chr10 135534747 1793333212 13.231538418705279 466.8509249393362 chr11 135006516 1169785764 8.664661519004015 27.141122251861322 chr12 133851895 1090582913 8.147683773920422 16.75533656296686 chr13 115169878 604619129 5.249802635025801 13.119475857238674 chr14 107349540 727119431 6.773381898050052 28.912967899381737 chr15 102531392 796720872 7.770506734171716 14.238197019372747 chr16 90354753 1231129812 13.6255124509056 177.12280645248114 chr17 81195210 943479057 11.619885668132394 65.21804220894776 chr18 78077248 619530535 7.934840825844681 251.2429769658868 chr19 59128983 922491406 15.601340648798239 36.91189072937462 chr20 63025520 700934741 11.121443202689958 145.78628071283092 chr21 48129895 455503620 9.464047656866901 196.165986986664 chr22 51304566 509615525 9.933141720758343 28.800135173502536 chrMT 16571 10496502 633.4259851547885 283.1255758867765 chrX 155270560 1326344362 8.542149664430914 18.638182065301336 chrY 59373566 438910929 7.392362604597474 520.7964675979991