BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080902.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 = 4,079,673 number of mapped reads = 3,710,284 (90.95%) number of supplementary alignments = 39,822 (0.98%) number of secondary alignments = 0 number of mapped bases = 254,967,692 bp number of sequenced bases = 254,873,591 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,498 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7954 >>>>>>> ACTG content number of A's = 73,339,907 bp (28.78%) number of C's = 45,311,001 bp (17.78%) number of T's = 81,285,032 bp (31.89%) number of G's = 53,721,250 bp (21.08%) number of N's = 1,216,401 bp (0.48%) GC percentage = 38.86% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 2,865,436 number of insertions = 19,215 mapped reads with insertion percentage = 0.51% number of deletions = 57,653 mapped reads with deletion percentage = 1.54% homopolymer indels = 50.27% >>>>>>> Coverage mean coverageData = 0.0824X std coverageData = 0.5322X There is a 6.06% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 20157797 0.08087360793375917 0.7870800327215913 chr2 243199373 22149225 0.0910743507550079 0.5329555183333629 chr3 198022430 18150095 0.09165676332726551 0.38958554130075695 chr4 191154276 17748553 0.09284936424859258 0.4026133915658711 chr5 180915260 15494739 0.08564639047032295 0.378044022571925 chr6 171115067 15590205 0.0911094813176212 0.47050088172611404 chr7 159138663 14165543 0.08901383694545681 0.7553001934698284 chr8 146364022 12941955 0.08842306205550979 0.9272078089661481 chr9 141213431 10800791 0.076485578769062 0.5057174342765085 chr10 135534747 11428756 0.08432343921370954 0.46199514794508845 chr11 135006516 11291440 0.08363625945284003 0.4826445203026003 chr12 133851895 11106288 0.08297445471354739 0.3764118083270391 chr13 115169878 9080577 0.07884506919422107 0.36166627183727396 chr14 107349540 7968194 0.0742266245388662 0.3796103146320208 chr15 102531392 7184583 0.07007203218308009 0.3401245936319945 chr16 90354753 6362622 0.07041823245313945 0.3674227931291898 chr17 81195210 5953487 0.07332313076103873 0.4098389099220857 chr18 78077248 7035236 0.09010609595256226 0.8839820212282646 chr19 59128983 3843259 0.06499788775328674 0.5528200944535757 chr20 63025520 4832567 0.07667635269014837 0.3679870092603699 chr21 48129895 3283150 0.06821436032636265 0.36234666796373366 chr22 51304566 2433349 0.047429482202422296 0.27932582914425896 chrMT 16571 11832 0.7140184659948102 1.1002341096950528 chrX 155270560 15408392 0.09923575982465704 0.42632103346541783 chrY 59373566 545057 0.009180129083033348 0.16115246425271504