BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617423.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,082,792 (94.01%) number of supplementary alignments = 490,991 (1.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,186,146 number of mapped paired reads (second in pair) = 14,896,646 number of mapped paired reads (both in pair) = 29,485,068 number of mapped paired reads (singletons) = 597,724 number of mapped bases = 2,960,726,645 bp number of sequenced bases = 2,960,074,353 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,418,828 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 60,053.7038 std insert size = 2,335,780.4879 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 53.8812 >>>>>>> ACTG content number of A's = 883,848,250 bp (29.86%) number of C's = 594,623,168 bp (20.09%) number of T's = 875,751,640 bp (29.59%) number of G's = 605,410,249 bp (20.45%) number of N's = 441,046 bp (0.01%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 26,865,353 number of insertions = 243,343 mapped reads with insertion percentage = 0.8% number of deletions = 289,602 mapped reads with deletion percentage = 0.94% homopolymer indels = 45.04% >>>>>>> Coverage mean coverageData = 0.9564X std coverageData = 2.9404X There is a 29.6% of reference with a coverageData >= 1X There is a 17.01% of reference with a coverageData >= 2X There is a 10.9% of reference with a coverageData >= 3X There is a 7.55% of reference with a coverageData >= 4X There is a 5.48% of reference with a coverageData >= 5X There is a 4.13% of reference with a coverageData >= 6X There is a 3.2% of reference with a coverageData >= 7X There is a 2.53% of reference with a coverageData >= 8X There is a 2.04% of reference with a coverageData >= 9X There is a 1.67% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.16% of reference with a coverageData >= 12X There is a 0.98% of reference with a coverageData >= 13X There is a 0.83% of reference with a coverageData >= 14X There is a 0.72% of reference with a coverageData >= 15X There is a 0.62% of reference with a coverageData >= 16X There is a 0.54% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 190545909 0.7644751625312901 2.7553729579945894 chr2 243199373 294924145 1.212684643722334 3.125399453404487 chr3 198022430 249911806 1.262037871164393 3.4292098713411354 chr4 191154276 141995972 0.7428344004190626 2.2894350103322862 chr5 180915260 189235640 1.0459904819527108 2.869781142101018 chr6 171115067 135577943 0.7923203104025901 2.600308343501149 chr7 159138663 221531402 1.3920652456405267 3.2468671758156447 chr8 146364022 131117734 0.8958330893639969 3.2605383766143587 chr9 141213431 118371962 0.8382486082361387 2.6212566838744804 chr10 135534747 94977598 0.700761982460483 2.4253131433604653 chr11 135006516 220074198 1.630100564923844 3.8502030249655115 chr12 133851895 141478109 1.0569750170514955 2.8096771194951233 chr13 115169878 128349417 1.1144356426252358 2.7813653341477567 chr14 107349540 85824037 0.7994821123593078 2.8933666367614266 chr15 102531392 68008270 0.6632921749467714 2.3886671126067496 chr16 90354753 74805833 0.827912539365804 3.3377379055728515 chr17 81195210 91175267 1.1229143566473934 3.722750917150188 chr18 78077248 42489038 0.5441923106716057 2.0224749452371715 chr19 59128983 42517224 0.7190589427184972 2.3550977187885715 chr20 63025520 100969900 1.6020478688632795 4.758121223589492 chr21 48129895 40358999 0.8385432588207392 2.526221610984224 chr22 51304566 23937807 0.4665823895674315 2.0869984513953392 chrMT 16571 188941 11.401906945869289 5.654394488056629 chrX 155270560 129963032 0.8370101325067676 2.5824633907848003 chrY 59373566 2396462 0.040362440079815994 0.6309514722644823