BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472613.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 = 19,833,832 number of mapped reads = 19,631,133 (98.98%) number of supplementary alignments = 96,128 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,855,387 number of mapped paired reads (second in pair) = 9,775,746 number of mapped paired reads (both in pair) = 19,486,650 number of mapped paired reads (singletons) = 144,483 number of mapped bases = 1,929,201,330 bp number of sequenced bases = 1,928,967,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,836,275 duplication rate = 50.69% >>>>>>> Insert size mean insert size = 22,283.898 std insert size = 1,494,347.3773 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.8281 >>>>>>> ACTG content number of A's = 515,666,188 bp (26.73%) number of C's = 451,205,099 bp (23.39%) number of T's = 516,329,308 bp (26.77%) number of G's = 445,409,329 bp (23.09%) number of N's = 357,881 bp (0.02%) GC percentage = 46.48% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 11,972,816 number of insertions = 121,929 mapped reads with insertion percentage = 0.62% number of deletions = 100,336 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 0.6232X std coverageData = 26.4044X There is a 3.84% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 300420593 1.205295263838079 49.80943863667293 chr2 243199373 138403456 0.5690946250918172 24.19523647499364 chr3 198022430 121187086 0.611986662319011 16.296504435974 chr4 191154276 41301039 0.21606128758532192 9.77950131783621 chr5 180915260 77855007 0.43033963525243807 17.570534007799303 chr6 171115067 195466722 1.1423115768057994 33.26386047924883 chr7 159138663 110862026 0.69663791256057 28.569365601110544 chr8 146364022 70809541 0.4837906203479432 15.98650123988727 chr9 141213431 96494732 0.6833254550694969 20.055686748188354 chr10 135534747 57448828 0.4238678956622098 18.934512019619834 chr11 135006516 56001487 0.41480580833594727 29.245151797312616 chr12 133851895 61448334 0.4590770567723378 16.3270170770977 chr13 115169878 74101742 0.643412524931215 25.3287580212399 chr14 107349540 27382065 0.25507389225887694 12.265288602843144 chr15 102531392 25832906 0.25195118778841896 8.829953476109216 chr16 90354753 108898090 1.20522813005753 53.07295662484816 chr17 81195210 84394864 1.0394069305319857 24.550377448339415 chr18 78077248 20607610 0.2639387341111203 11.821334244505401 chr19 59128983 45757320 0.773856029284319 20.779992363890674 chr20 63025520 85047341 1.349411175028782 37.357518520459905 chr21 48129895 20806829 0.43230572183878646 26.892703544020353 chr22 51304566 25652023 0.49999493222494074 31.3302313207862 chrMT 16571 3340 0.20155693681733147 0.599629909441355 chrX 155270560 82071188 0.5285688929053904 17.255037876998834 chrY 59373566 947161 0.015952570542924777 0.6927011056728267