BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081122.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,529,577 number of mapped reads = 2,335,178 (92.31%) number of supplementary alignments = 15,260 (0.6%) number of secondary alignments = 0 number of mapped bases = 160,208,549 bp number of sequenced bases = 160,145,491 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,319 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1777 >>>>>>> ACTG content number of A's = 45,360,134 bp (28.32%) number of C's = 30,926,174 bp (19.31%) number of T's = 48,998,514 bp (30.6%) number of G's = 34,858,829 bp (21.77%) number of N's = 1,840 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,446,064 number of insertions = 13,201 mapped reads with insertion percentage = 0.56% number of deletions = 35,196 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.0518X std coverageData = 0.5822X There is a 4.37% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13070807 0.05244041899498417 0.9080778487789817 chr2 243199373 11783767 0.04845311422739564 0.6732631604905112 chr3 198022430 13415973 0.06774976450900032 0.3010074288371863 chr4 191154276 9524433 0.0498258956027748 0.3175245656220823 chr5 180915260 9072924 0.05015013106135989 0.2654417483593316 chr6 171115067 13624635 0.07962264947714978 0.6358352448059263 chr7 159138663 7765015 0.04879401933897107 0.7744115586148904 chr8 146364022 10667654 0.07288440051203293 0.5591467265529857 chr9 141213431 7685920 0.05442768400691291 0.7780245961234817 chr10 135534747 7403392 0.05462357191694909 0.4764912440710362 chr11 135006516 7072277 0.052384708601768526 0.468177690278658 chr12 133851895 7743588 0.05785191162217016 0.3247666389032927 chr13 115169878 3826179 0.03322204613258338 0.202154372357184 chr14 107349540 4754413 0.044289085915039786 0.42431188707676537 chr15 102531392 3609473 0.03520358916028371 0.22201734387190944 chr16 90354753 4125155 0.045655096860261465 0.4038881911523615 chr17 81195210 3743902 0.04610988751676361 0.27842718781026676 chr18 78077248 4175320 0.0534767823783953 1.5898852581566425 chr19 59128983 3488521 0.05899849486672213 0.700763809450792 chr20 63025520 2682322 0.04255929978840317 0.2932313664937551 chr21 48129895 3875192 0.0805152805756173 0.46179150788516127 chr22 51304566 1566122 0.030525976966650492 0.1943640760085709 chrMT 16571 159192 9.60666224126486 6.006489817042295 chrX 155270560 4936663 0.031793940847511595 0.296438656244982 chrY 59373566 435710 0.007338450919387257 0.21868102874085316