BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472618.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 = 21,438,916 number of mapped reads = 21,256,551 (99.15%) number of supplementary alignments = 102,680 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,667,367 number of mapped paired reads (second in pair) = 10,589,184 number of mapped paired reads (both in pair) = 21,129,708 number of mapped paired reads (singletons) = 126,843 number of mapped bases = 2,091,540,267 bp number of sequenced bases = 2,091,249,856 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,218,006 duplication rate = 51.29% >>>>>>> Insert size mean insert size = 21,763.2294 std insert size = 1,495,173.9139 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 54.7904 >>>>>>> ACTG content number of A's = 556,525,615 bp (26.61%) number of C's = 492,150,627 bp (23.53%) number of T's = 557,849,407 bp (26.68%) number of G's = 484,340,927 bp (23.16%) number of N's = 383,280 bp (0.02%) GC percentage = 46.69% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 12,856,429 number of insertions = 119,053 mapped reads with insertion percentage = 0.56% number of deletions = 117,178 mapped reads with deletion percentage = 0.55% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.6756X std coverageData = 27.807X There is a 4.01% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% 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 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% 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 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 269463157 1.0810932222311294 35.21920601355313 chr2 243199373 130590989 0.5369709115162892 19.651640464728064 chr3 198022430 168644229 0.8516420538824819 30.162189634571003 chr4 191154276 38746598 0.20269804479811898 9.742175753789926 chr5 180915260 135350801 0.7481447446721742 45.17104510693132 chr6 171115067 213911754 1.2501047263126164 42.25863821793921 chr7 159138663 89969353 0.565351947188346 21.705930769476545 chr8 146364022 143938543 0.9834284480102631 37.906306397335015 chr9 141213431 95466221 0.6760420756294775 18.066227235610167 chr10 135534747 65663274 0.484475571419335 24.754227529804655 chr11 135006516 46427205 0.3438886238646437 12.818960729445536 chr12 133851895 54116922 0.4043044889278557 13.607876720107134 chr13 115169878 72681052 0.6310769209983882 21.919153493510777 chr14 107349540 20819787 0.19394388648521457 7.9865748748467125 chr15 102531392 24115091 0.23519714820608306 11.675687258619185 chr16 90354753 94342590 1.0441353317627906 36.292173482720486 chr17 81195210 78859526 0.9712337217922091 23.847314575557427 chr18 78077248 31933355 0.4089969333960131 24.828385747255993 chr19 59128983 61617536 1.042086856119274 26.28751591557997 chr20 63025520 96386409 1.5293235026065632 52.28135307885549 chr21 48129895 14468845 0.30062074725074717 17.538683475862694 chr22 51304566 31148998 0.6071389045567601 19.579679732273032 chrMT 16571 4000 0.24138555307464848 0.5832151147874628 chrX 155270560 110450475 0.7113420277482093 27.551533826541036 chrY 59373566 2423557 0.04081878794344271 3.877761201830949