BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926892.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 22,826,066 number of mapped reads = 22,371,459 (98.01%) number of supplementary alignments = 50,243 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,240,896 number of mapped paired reads (second in pair) = 11,130,563 number of mapped paired reads (both in pair) = 22,208,310 number of mapped paired reads (singletons) = 163,149 number of mapped bases = 2,155,938,895 bp number of sequenced bases = 2,154,382,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,365,139 duplication rate = 5.21% >>>>>>> Insert size mean insert size = 30,977.3187 std insert size = 1,725,725.2779 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 54.147 >>>>>>> ACTG content number of A's = 605,825,649 bp (28.12%) number of C's = 451,791,485 bp (20.97%) number of T's = 605,619,554 bp (28.11%) number of G's = 490,931,827 bp (22.79%) number of N's = 214,458 bp (0.01%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 20,907,406 number of insertions = 319,606 mapped reads with insertion percentage = 1.41% number of deletions = 1,129,712 mapped reads with deletion percentage = 4.92% homopolymer indels = 53.4% >>>>>>> Coverage mean coverageData = 0.6964X std coverageData = 2.2419X There is a 24.98% of reference with a coverageData >= 1X There is a 14.24% of reference with a coverageData >= 2X There is a 8.61% of reference with a coverageData >= 3X There is a 5.67% of reference with a coverageData >= 4X There is a 3.89% of reference with a coverageData >= 5X There is a 2.76% of reference with a coverageData >= 6X There is a 2.01% of reference with a coverageData >= 7X There is a 1.5% of reference with a coverageData >= 8X There is a 1.13% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.53% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% 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 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 196353396 0.7877749520230884 2.555918173792122 chr2 243199373 184079386 0.7569073214674776 3.288596627687107 chr3 198022430 146606557 0.7403532872513482 1.9198218010790247 chr4 191154276 113552062 0.5940335961932653 1.684127857391863 chr5 180915260 128978470 0.7129220055842719 1.8806421882472388 chr6 171115067 132817507 0.7761882651748019 1.9820656317533942 chr7 159138663 93974783 0.5905213807156341 1.9001635652318332 chr8 146364022 116923355 0.7988531156925983 2.096520976753583 chr9 141213431 85553727 0.6058469537504545 2.7352953653796956 chr10 135534747 111882927 0.8254925727643849 2.3127741916647953 chr11 135006516 110015817 0.8148926456260822 2.212740476928111 chr12 133851895 86426305 0.64568607713772 1.892516838166869 chr13 115169878 65956334 0.5726873653543334 1.6655059034574895 chr14 107349540 71355537 0.6647027737613035 1.9207389746094088 chr15 102531392 72601573 0.708091166849661 2.0122824805087682 chr16 90354753 51840427 0.5737432207910523 2.7688034363468566 chr17 81195210 61588180 0.7585198683518399 2.1570544454041456 chr18 78077248 58887375 0.754219398204199 2.952358395129175 chr19 59128983 38633997 0.6533851089574803 2.07766615199629 chr20 63025520 55194519 0.8757487284515859 2.3246140382953286 chr21 48129895 30693110 0.6377140444623867 2.2297137881845024 chr22 51304566 29976353 0.5842823619246676 1.8881641013798602 chrMT 16571 25445 1.5355138494961076 2.266123831949115 chrX 155270560 109428792 0.7047620102613141 1.9279677822969579 chrY 59373566 2592961 0.043671976852459896 0.9450895922283596