BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927053.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 = 31,665,140 number of mapped reads = 31,043,332 (98.04%) number of supplementary alignments = 376,182 (1.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,587,410 number of mapped paired reads (second in pair) = 15,455,922 number of mapped paired reads (both in pair) = 30,727,166 number of mapped paired reads (singletons) = 316,166 number of mapped bases = 2,921,845,412 bp number of sequenced bases = 2,919,744,316 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,358,722 duplication rate = 6.02% >>>>>>> Insert size mean insert size = 122,387.7555 std insert size = 3,426,879.1962 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.4964 >>>>>>> ACTG content number of A's = 821,589,313 bp (28.14%) number of C's = 598,294,022 bp (20.49%) number of T's = 833,152,859 bp (28.54%) number of G's = 666,266,123 bp (22.82%) number of N's = 441,999 bp (0.02%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 31,070,068 number of insertions = 452,543 mapped reads with insertion percentage = 1.43% number of deletions = 1,489,029 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.6% >>>>>>> Coverage mean coverageData = 0.9438X std coverageData = 3.4709X There is a 34.61% of reference with a coverageData >= 1X There is a 20.26% of reference with a coverageData >= 2X There is a 12.31% of reference with a coverageData >= 3X There is a 7.93% of reference with a coverageData >= 4X There is a 5.26% of reference with a coverageData >= 5X There is a 3.58% of reference with a coverageData >= 6X There is a 2.48% of reference with a coverageData >= 7X There is a 1.74% of reference with a coverageData >= 8X There is a 1.24% of reference with a coverageData >= 9X There is a 0.9% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.48% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.16% 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 0.08% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 241829712 0.9702271193137769 4.893989581616951 chr2 243199373 252933728 1.0400262339492135 5.578684145670276 chr3 198022430 195543794 0.9874830543186446 1.9594685730822607 chr4 191154276 172331531 0.9015311328949817 2.7981690917876647 chr5 180915260 175696749 0.9711549429274235 1.9346267805945512 chr6 171115067 165630078 0.9679456105405376 1.9642464887600182 chr7 159138663 148126378 0.9308006942348134 2.6539463259168583 chr8 146364022 148894063 1.0172859488652204 2.3993415251899517 chr9 141213431 129710648 0.9185432793570464 4.5815019182510754 chr10 135534747 143127803 1.0560229473848504 5.229988161435743 chr11 135006516 140985167 1.0442841662546125 3.613355123737114 chr12 133851895 128934939 0.963265697508429 1.9711726129276301 chr13 115169878 87366227 0.7585857388856485 1.7172282195669848 chr14 107349540 87883682 0.8186684544712535 1.886982238664401 chr15 102531392 86218071 0.8408943770118716 1.8835232694533972 chr16 90354753 94660034 1.0476486389155422 4.890173299499144 chr17 81195210 80800850 0.9951430632422774 2.6540021797913336 chr18 78077248 77349883 0.9906840338429961 4.784880393070829 chr19 59128983 50050130 0.8464568044405567 3.1098415932117995 chr20 63025520 70381733 1.11671800565866 2.362860693756087 chr21 48129895 37365215 0.7763410869689202 2.850333436588277 chr22 51304566 38947455 0.7591420810381673 1.956173129186919 chrMT 16571 2471041 149.1183996137831 108.12575599607516 chrX 155270560 159332036 1.0261574119395203 2.3124651399243095 chrY 59373566 5274465 0.08883524024816027 3.3686061258096536