BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472568.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 = 309,681,210 number of mapped reads = 304,471,048 (98.32%) number of supplementary alignments = 217,875 (0.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 152,926,302 number of mapped paired reads (second in pair) = 151,544,746 number of mapped paired reads (both in pair) = 302,545,466 number of mapped paired reads (singletons) = 1,925,582 number of mapped bases = 29,021,120,410 bp number of sequenced bases = 29,016,004,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,963,731 duplication rate = 53.73% >>>>>>> Insert size mean insert size = 8,370.5116 std insert size = 842,762.3123 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 51.64 >>>>>>> ACTG content number of A's = 7,029,455,224 bp (24.23%) number of C's = 7,490,060,242 bp (25.81%) number of T's = 7,108,843,940 bp (24.5%) number of G's = 7,381,928,407 bp (25.44%) number of N's = 5,716,296 bp (0.02%) GC percentage = 51.25% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 308,299,985 number of insertions = 2,094,369 mapped reads with insertion percentage = 0.67% number of deletions = 2,119,546 mapped reads with deletion percentage = 0.68% homopolymer indels = 37.84% >>>>>>> Coverage mean coverageData = 9.3747X std coverageData = 103.2919X There is a 65.29% of reference with a coverageData >= 1X There is a 54.98% of reference with a coverageData >= 2X There is a 44.34% of reference with a coverageData >= 3X There is a 37.35% of reference with a coverageData >= 4X There is a 30.38% of reference with a coverageData >= 5X There is a 25.72% of reference with a coverageData >= 6X There is a 21.22% of reference with a coverageData >= 7X There is a 18.12% of reference with a coverageData >= 8X There is a 15.24% of reference with a coverageData >= 9X There is a 13.18% of reference with a coverageData >= 10X There is a 11.35% of reference with a coverageData >= 11X There is a 10.01% of reference with a coverageData >= 12X There is a 8.84% of reference with a coverageData >= 13X There is a 7.97% of reference with a coverageData >= 14X There is a 7.22% of reference with a coverageData >= 15X There is a 6.64% of reference with a coverageData >= 16X There is a 6.15% of reference with a coverageData >= 17X There is a 5.76% of reference with a coverageData >= 18X There is a 5.42% of reference with a coverageData >= 19X There is a 5.15% of reference with a coverageData >= 20X There is a 4.92% of reference with a coverageData >= 21X There is a 4.72% of reference with a coverageData >= 22X There is a 4.55% of reference with a coverageData >= 23X There is a 4.41% of reference with a coverageData >= 24X There is a 4.27% of reference with a coverageData >= 25X There is a 4.16% of reference with a coverageData >= 26X There is a 4.05% of reference with a coverageData >= 27X There is a 3.96% of reference with a coverageData >= 28X There is a 3.87% of reference with a coverageData >= 29X There is a 3.79% of reference with a coverageData >= 30X There is a 3.72% of reference with a coverageData >= 31X There is a 3.65% of reference with a coverageData >= 32X There is a 3.58% of reference with a coverageData >= 33X There is a 3.52% of reference with a coverageData >= 34X There is a 3.46% of reference with a coverageData >= 35X There is a 3.4% of reference with a coverageData >= 36X There is a 3.35% of reference with a coverageData >= 37X There is a 3.3% of reference with a coverageData >= 38X There is a 3.25% of reference with a coverageData >= 39X There is a 3.21% of reference with a coverageData >= 40X There is a 3.16% of reference with a coverageData >= 41X There is a 3.12% of reference with a coverageData >= 42X There is a 3.08% of reference with a coverageData >= 43X There is a 3.04% of reference with a coverageData >= 44X There is a 3% of reference with a coverageData >= 45X There is a 2.96% of reference with a coverageData >= 46X There is a 2.92% of reference with a coverageData >= 47X There is a 2.89% of reference with a coverageData >= 48X There is a 2.85% of reference with a coverageData >= 49X There is a 2.82% of reference with a coverageData >= 50X There is a 2.78% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2810649939 11.27640094826484 92.88113012716032 chr2 243199373 1937253506 7.965701071112548 74.0335392511195 chr3 198022430 1517810810 7.664842866537897 46.38120461084795 chr4 191154276 1216049801 6.361614432313301 55.13715384801191 chr5 180915260 1427187128 7.88870506556495 71.19322620491789 chr6 171115067 1315099562 7.685469111846241 42.7900686567127 chr7 159138663 1943090542 12.210046919899032 327.5048354477187 chr8 146364022 1558403638 10.647450218333027 174.4167861961775 chr9 141213431 1281726905 9.076522650313624 51.73990429551676 chr10 135534747 1229664870 9.072690931425873 67.47298416970116 chr11 135006516 1464191958 10.845342887005543 52.42798383455986 chr12 133851895 1227015571 9.166964509542431 39.89283353338726 chr13 115169878 558262910 4.847299655904819 24.726208155246624 chr14 107349540 773919897 7.2093452566261575 37.508658030517324 chr15 102531392 1181481661 11.523121240761073 64.52189401663863 chr16 90354753 1312276940 14.52360718644209 73.68785395120554 chr17 81195210 1476229914 18.181243868942516 101.85217656637701 chr18 78077248 524948214 6.723446681932232 63.03727803849293 chr19 59128983 1517897510 25.670955815357082 101.45005228440303 chr20 63025520 691079510 10.965074306407944 59.92323336826603 chr21 48129895 382531532 7.947898743597924 65.5371413425078 chr22 51304566 748858754 14.596337370829723 81.02217752259148 chrMT 16571 2140949 129.1985396174039 46.43742249753079 chrX 155270560 653110982 4.2062769787138015 22.65658288339934 chrY 59373566 270237407 4.551476780087624 83.6462096815951