BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472410.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 = 18,745,754 number of mapped reads = 18,589,291 (99.17%) number of supplementary alignments = 76,983 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,319,881 number of mapped paired reads (second in pair) = 9,269,410 number of mapped paired reads (both in pair) = 18,493,892 number of mapped paired reads (singletons) = 95,399 number of mapped bases = 1,821,568,475 bp number of sequenced bases = 1,821,348,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,041,174 duplication rate = 46.72% >>>>>>> Insert size mean insert size = 19,408.6072 std insert size = 1,369,521.4512 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 54.6325 >>>>>>> ACTG content number of A's = 493,983,747 bp (27.12%) number of C's = 417,828,208 bp (22.94%) number of T's = 494,779,806 bp (27.17%) number of G's = 414,540,971 bp (22.76%) number of N's = 215,772 bp (0.01%) GC percentage = 45.7% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 9,988,926 number of insertions = 113,976 mapped reads with insertion percentage = 0.61% number of deletions = 95,854 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.5884X std coverageData = 20.4107X There is a 5.34% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.5% 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 0.2% 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 0.18% 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 0.17% 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 207207314 0.8313211544616372 22.26568215940882 chr2 243199373 179035914 0.7361693074759695 27.8012568939577 chr3 198022430 63070578 0.3185021918981602 8.989952784153857 chr4 191154276 107047971 0.560008246951274 24.442374611017467 chr5 180915260 145149249 0.8023051731512312 28.6741567920401 chr6 171115067 104419374 0.6102289870242694 14.671732321806886 chr7 159138663 100710782 0.6328492404136887 18.621233055626718 chr8 146364022 96130486 0.6567904098727213 15.996560179097266 chr9 141213431 111403948 0.7889047607659926 19.0591731446469 chr10 135534747 74489054 0.5495937805528202 20.17988981940465 chr11 135006516 73231278 0.5424277299326797 18.415566954291368 chr12 133851895 61388004 0.4586263347261539 21.170590167396174 chr13 115169878 43397135 0.3768097679151835 17.223480940993106 chr14 107349540 62695522 0.584031585044519 24.20548310443498 chr15 102531392 42333769 0.4128859286334472 18.103897309732385 chr16 90354753 98665638 1.091980606709201 32.42815168998594 chr17 81195210 68158927 0.8394451717040944 16.70649845933668 chr18 78077248 45483504 0.5825449175667667 25.899342919551273 chr19 59128983 21001883 0.35518762431614964 8.25456118058166 chr20 63025520 35171556 0.5580526110692938 14.886072156669123 chr21 48129895 15631089 0.32476881572253585 14.834811029318894 chr22 51304566 27893115 0.5436770481598071 15.212716517137148 chrMT 16571 8316 0.5018405648421942 0.9222603160245314 chrX 155270560 37420513 0.24100198389185948 10.17596157975991 chrY 59373566 423556 0.007133747028096645 0.745954396376991