BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083669.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 = 1,432,631 number of mapped reads = 1,068,350 (74.57%) number of supplementary alignments = 5,969 (0.42%) number of secondary alignments = 0 number of mapped bases = 66,718,213 bp number of sequenced bases = 66,696,773 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,722 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4688 >>>>>>> ACTG content number of A's = 19,609,118 bp (29.4%) number of C's = 12,502,358 bp (18.75%) number of T's = 19,782,079 bp (29.66%) number of G's = 14,799,030 bp (22.19%) number of N's = 4,188 bp (0.01%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 591,171 number of insertions = 4,804 mapped reads with insertion percentage = 0.45% number of deletions = 13,365 mapped reads with deletion percentage = 1.24% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.2115X There is a 2% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 6237112 0.02502345621036587 0.4537259871471136 chr2 243199373 7614199 0.03130846476318835 0.20730773852278284 chr3 198022430 5823193 0.029406734378524695 0.18309471691646625 chr4 191154276 3219955 0.016844797131297235 0.13819084051735242 chr5 180915260 3488576 0.019282928372100838 0.14691193617126047 chr6 171115067 4773495 0.027896403769049748 0.19281124429718 chr7 159138663 3772151 0.023703548395401564 0.22935537896582558 chr8 146364022 3894104 0.026605609403108643 0.23671939752266546 chr9 141213431 2980370 0.021105428703874492 0.16409038707562187 chr10 135534747 3269999 0.02412664702137231 0.20699943846003122 chr11 135006516 2162724 0.01601940457451698 0.14210232251280266 chr12 133851895 2535311 0.018941166279341805 0.14622746574487505 chr13 115169878 1934709 0.01679874142091216 0.13644577047351195 chr14 107349540 1289326 0.012010540520248154 0.11635871359631159 chr15 102531392 1700474 0.01658491089246111 0.13578081697761174 chr16 90354753 2029433 0.02246072212714698 0.16155305472355017 chr17 81195210 1503157 0.01851287779168254 0.1467833070611203 chr18 78077248 1706362 0.021854791808235866 0.21616138421654751 chr19 59128983 1736632 0.029370232868710086 0.29263249241846995 chr20 63025520 1109237 0.01759980718921478 0.14119607666642595 chr21 48129895 972557 0.020206921290811045 0.15175129008388685 chr22 51304566 597962 0.011655141961438676 0.11318048777783271 chrMT 16571 37557 2.2664293042061434 2.061283913334109 chrX 155270560 2208629 0.014224389993827549 0.12874891054534587 chrY 59373566 120989 0.002037758688774058 0.054264682644046526