BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617498.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,555,524 (95.49%) number of supplementary alignments = 137,497 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,353,013 number of mapped paired reads (second in pair) = 15,202,511 number of mapped paired reads (both in pair) = 30,111,242 number of mapped paired reads (singletons) = 444,282 number of mapped bases = 2,983,196,741 bp number of sequenced bases = 2,981,432,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,273,493 duplication rate = 9.91% >>>>>>> Insert size mean insert size = 30,464.8379 std insert size = 1,614,683.3156 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 52.7895 >>>>>>> ACTG content number of A's = 879,803,816 bp (29.51%) number of C's = 602,841,557 bp (20.22%) number of T's = 879,168,411 bp (29.49%) number of G's = 617,601,538 bp (20.71%) number of N's = 2,017,261 bp (0.07%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 36,927,411 number of insertions = 441,811 mapped reads with insertion percentage = 1.42% number of deletions = 1,036,220 mapped reads with deletion percentage = 3.32% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.9637X std coverageData = 9.7568X There is a 38.27% of reference with a coverageData >= 1X There is a 20.7% of reference with a coverageData >= 2X There is a 11.7% of reference with a coverageData >= 3X There is a 6.96% of reference with a coverageData >= 4X There is a 4.3% of reference with a coverageData >= 5X There is a 2.76% of reference with a coverageData >= 6X There is a 1.82% of reference with a coverageData >= 7X There is a 1.25% of reference with a coverageData >= 8X There is a 0.88% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192280497 0.7714343748816578 9.542364210835974 chr2 243199373 308153643 1.2670823908744206 11.534515734715617 chr3 198022430 246380763 1.24420634066555 2.243426595230204 chr4 191154276 154198627 0.8066710838317841 6.172954762449765 chr5 180915260 190677987 1.0539629824482468 2.0818275840156337 chr6 171115067 140301667 0.8199258514155273 5.431131717528345 chr7 159138663 230252159 1.4468649834012994 13.191736405009902 chr8 146364022 132655822 0.9063417374523911 3.886301916835493 chr9 141213431 123323824 0.8733151168885628 18.425781545209155 chr10 135534747 126232860 0.9313689868768487 18.686792827585265 chr11 135006516 168413986 1.2474507971156 12.64440120427876 chr12 133851895 130371638 0.9739991951552124 1.9948985692580978 chr13 115169878 126564124 1.0989342543195193 2.1279801946173613 chr14 107349540 86602339 0.806732278498818 2.2149475262677027 chr15 102531392 67275439 0.6561447931966046 1.4523612915590347 chr16 90354753 80764211 0.8938568068466747 15.05803517658933 chr17 81195210 83352821 1.0265731315923685 13.833713398974703 chr18 78077248 53471747 0.684856963708557 17.125724426909155 chr19 59128983 35581450 0.6017598848267016 5.891337506353201 chr20 63025520 88049659 1.3970477197173463 2.769598625343545 chr21 48129895 43071333 0.8948977137805931 3.8404163252759007 chr22 51304566 22354098 0.4357136166009084 1.2509684774220333 chrMT 16571 2107929 127.20590187677267 95.80395318290338 chrX 155270560 140437929 0.9044723545790007 4.163846640064458 chrY 59373566 10320189 0.17381790745059847 13.866704656574456