BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472612.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,782,442 number of mapped reads = 14,674,596 (99.27%) number of supplementary alignments = 67,059 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,353,109 number of mapped paired reads (second in pair) = 7,321,487 number of mapped paired reads (both in pair) = 14,604,262 number of mapped paired reads (singletons) = 70,334 number of mapped bases = 1,442,132,764 bp number of sequenced bases = 1,441,929,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,610,554 duplication rate = 49.23% >>>>>>> Insert size mean insert size = 19,655.4892 std insert size = 1,380,048.2731 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 54.7969 >>>>>>> ACTG content number of A's = 381,549,274 bp (26.46%) number of C's = 341,254,872 bp (23.67%) number of T's = 382,698,951 bp (26.54%) number of G's = 336,170,951 bp (23.31%) number of N's = 255,152 bp (0.02%) GC percentage = 46.98% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 8,827,962 number of insertions = 85,929 mapped reads with insertion percentage = 0.58% number of deletions = 85,877 mapped reads with deletion percentage = 0.57% homopolymer indels = 43.82% >>>>>>> Coverage mean coverageData = 0.4659X std coverageData = 17.1192X There is a 3.21% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 241071717 0.9671860235806594 29.027351646455774 chr2 243199373 91089073 0.37454485131423426 13.994484131637261 chr3 198022430 118054708 0.5961683633515658 18.73468471228673 chr4 191154276 26929551 0.1408786220403461 8.213913607186688 chr5 180915260 58068414 0.3209702376681768 11.666092026554415 chr6 171115067 121750316 0.7115113714679491 17.92079912785854 chr7 159138663 76108992 0.47825582146558565 20.699543957713235 chr8 146364022 60453369 0.41303435211694306 13.295290711167771 chr9 141213431 70939999 0.5023601402334031 16.974366174727752 chr10 135534747 29584789 0.21828195097453496 8.718290260381522 chr11 135006516 41959402 0.3107953841279779 11.749266532481697 chr12 133851895 55108123 0.4117096960039303 11.428055296229097 chr13 115169878 52074482 0.45215366122034095 20.77046528461493 chr14 107349540 12835074 0.11956338145463874 3.9735457622621926 chr15 102531392 28329750 0.2763031833216504 11.046441112111792 chr16 90354753 70311278 0.7781691130293943 23.506575896877784 chr17 81195210 59193532 0.7290273896699079 19.33448624190343 chr18 78077248 29861347 0.3824590103380693 18.691460342050625 chr19 59128983 37796838 0.6392269253134287 17.09874574537259 chr20 63025520 67193467 1.0661311005446683 30.59753827621654 chr21 48129895 12501412 0.25974318040793565 17.001644335424565 chr22 51304566 17803239 0.34701080991504735 12.972460496207828 chrMT 16571 885 0.05340655361776598 0.33174663899026846 chrX 155270560 62283183 0.4011268008565178 15.219286443329562 chrY 59373566 829824 0.013976320708107712 0.596027042263992