BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504631.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 = 566,538,364 number of mapped reads = 481,718,823 (85.03%) number of supplementary alignments = 4,165,015 (0.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 247,278,238 number of mapped paired reads (second in pair) = 234,440,585 number of mapped paired reads (both in pair) = 456,062,266 number of mapped paired reads (singletons) = 25,656,557 number of mapped bases = 45,261,336,026 bp number of sequenced bases = 45,224,532,380 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,602,519 duplication rate = 22.87% >>>>>>> Insert size mean insert size = 103,323.5681 std insert size = 2,990,313.8098 median insert size = 353 >>>>>>> Mapping quality mean mapping quality = 51.4887 >>>>>>> ACTG content number of A's = 12,337,919,234 bp (27.28%) number of C's = 10,239,525,264 bp (22.64%) number of T's = 12,431,949,087 bp (27.49%) number of G's = 10,184,662,597 bp (22.52%) number of N's = 30,476,198 bp (0.07%) GC percentage = 45.16% >>>>>>> Mismatches and indels general error rate = 0.0261 number of mismatches = 1,135,455,157 number of insertions = 12,409,141 mapped reads with insertion percentage = 2.4% number of deletions = 11,380,351 mapped reads with deletion percentage = 2.21% homopolymer indels = 33.16% >>>>>>> Coverage mean coverageData = 14.6207X std coverageData = 309.1136X There is a 87.06% of reference with a coverageData >= 1X There is a 81.81% of reference with a coverageData >= 2X There is a 76.2% of reference with a coverageData >= 3X There is a 70.79% of reference with a coverageData >= 4X There is a 65.64% of reference with a coverageData >= 5X There is a 60.83% of reference with a coverageData >= 6X There is a 56.37% of reference with a coverageData >= 7X There is a 52.26% of reference with a coverageData >= 8X There is a 48.46% of reference with a coverageData >= 9X There is a 44.96% of reference with a coverageData >= 10X There is a 41.74% of reference with a coverageData >= 11X There is a 38.76% of reference with a coverageData >= 12X There is a 36% of reference with a coverageData >= 13X There is a 33.46% of reference with a coverageData >= 14X There is a 31.1% of reference with a coverageData >= 15X There is a 28.92% of reference with a coverageData >= 16X There is a 26.89% of reference with a coverageData >= 17X There is a 25.01% of reference with a coverageData >= 18X There is a 23.27% of reference with a coverageData >= 19X There is a 21.65% of reference with a coverageData >= 20X There is a 20.15% of reference with a coverageData >= 21X There is a 18.75% of reference with a coverageData >= 22X There is a 17.46% of reference with a coverageData >= 23X There is a 16.25% of reference with a coverageData >= 24X There is a 15.14% of reference with a coverageData >= 25X There is a 14.1% of reference with a coverageData >= 26X There is a 13.13% of reference with a coverageData >= 27X There is a 12.24% of reference with a coverageData >= 28X There is a 11.41% of reference with a coverageData >= 29X There is a 10.64% of reference with a coverageData >= 30X There is a 9.92% of reference with a coverageData >= 31X There is a 9.26% of reference with a coverageData >= 32X There is a 8.64% of reference with a coverageData >= 33X There is a 8.07% of reference with a coverageData >= 34X There is a 7.54% of reference with a coverageData >= 35X There is a 7.05% of reference with a coverageData >= 36X There is a 6.59% of reference with a coverageData >= 37X There is a 6.16% of reference with a coverageData >= 38X There is a 5.77% of reference with a coverageData >= 39X There is a 5.4% of reference with a coverageData >= 40X There is a 5.06% of reference with a coverageData >= 41X There is a 4.74% of reference with a coverageData >= 42X There is a 4.45% of reference with a coverageData >= 43X There is a 4.18% of reference with a coverageData >= 44X There is a 3.92% of reference with a coverageData >= 45X There is a 3.69% of reference with a coverageData >= 46X There is a 3.47% of reference with a coverageData >= 47X There is a 3.26% of reference with a coverageData >= 48X There is a 3.07% of reference with a coverageData >= 49X There is a 2.9% of reference with a coverageData >= 50X There is a 2.73% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3198123369 12.830954467311036 103.76762218194534 chr2 243199373 3424228967 14.07992514437938 317.8151381460167 chr3 198022430 2343273620 11.833374734367213 36.23457568154474 chr4 191154276 3281315351 17.165796233613943 780.7010827056475 chr5 180915260 2815143325 15.560563133259185 44.3265148328681 chr6 171115067 1357548731 7.933542935760298 31.944144598127313 chr7 159138663 2131225539 13.392254897855967 50.041311468566064 chr8 146364022 2526835614 17.264048770127403 234.23982558954464 chr9 141213431 1185883464 8.397809299031904 148.73511760862064 chr10 135534747 3381681764 24.950662755138357 762.8425703155684 chr11 135006516 1840403702 13.631962045446755 36.657373727120394 chr12 133851895 1717706329 12.832887640477558 32.0940530587417 chr13 115169878 708304465 6.150084356258501 15.445839134654781 chr14 107349540 1167303233 10.87385407520144 37.79991687331312 chr15 102531392 1541923454 15.03854989113968 25.234880011446243 chr16 90354753 2384607882 26.391615303292348 312.02250626319693 chr17 81195210 1433613956 17.65638583852422 99.84403157677417 chr18 78077248 753337805 9.648621388397295 391.77003603296015 chr19 59128983 1710303648 28.924963042235987 63.043586686036036 chr20 63025520 1320916032 20.958431314807083 213.13370180647988 chr21 48129895 859560694 17.85918489953074 283.11037709638487 chr22 51304566 778774291 15.179434341185148 40.56325169015496 chrMT 16571 15158411 914.7553557419589 423.27520604962 chrX 155270560 2641386040 17.011505851463408 34.63109638004597 chrY 59373566 742776340 12.510219446815777 726.6933610858216