BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818735.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,342,416 number of mapped reads = 3,258,516 (97.49%) number of supplementary alignments = 23,073 (0.69%) number of secondary alignments = 0 number of mapped bases = 221,747,083 bp number of sequenced bases = 221,653,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,747,637 duplication rate = 43.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6332 >>>>>>> ACTG content number of A's = 64,634,949 bp (29.16%) number of C's = 46,513,523 bp (20.98%) number of T's = 63,983,261 bp (28.87%) number of G's = 46,506,930 bp (20.98%) number of N's = 14,693 bp (0.01%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,167,998 number of insertions = 27,120 mapped reads with insertion percentage = 0.82% number of deletions = 57,113 mapped reads with deletion percentage = 1.74% homopolymer indels = 41.93% >>>>>>> Coverage mean coverageData = 0.0716X std coverageData = 0.8512X There is a 2.76% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.92% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 18433925 0.07395738845521271 1.3205739979035636 chr2 243199373 19519720 0.08026221350496657 1.4058296248950808 chr3 198022430 15118408 0.07634694716149075 0.5901591227453891 chr4 191154276 14413704 0.07540351333809556 0.6783047207759468 chr5 180915260 13782924 0.0761844191584502 0.6098558418562448 chr6 171115067 12953559 0.07570086741689439 0.6624380961167987 chr7 159138663 12311563 0.07736374535206444 0.780368371845941 chr8 146364022 11201322 0.07653056978715712 0.696709530035495 chr9 141213431 9549122 0.06762191055325326 0.691256494246382 chr10 135534747 10781624 0.07954878168621955 0.8739865410633804 chr11 135006516 10579969 0.07836635825784882 0.6857762910163393 chr12 133851895 10305869 0.07699456925880653 0.6376244929764888 chr13 115169878 7041164 0.06113720116991007 0.5310121861591505 chr14 107349540 6880867 0.06409777815536051 0.6280844994282485 chr15 102531392 6337015 0.06180560778888089 0.5317093272176351 chr16 90354753 6600977 0.07305622317400391 0.9044593470386921 chr17 81195210 6067881 0.07473200697430304 0.6372274120887207 chr18 78077248 5971176 0.07647779798796187 0.8769777844997279 chr19 59128983 4297181 0.07267469829474321 1.0440684657210701 chr20 63025520 4794291 0.07606904314315852 0.6412895735380039 chr21 48129895 2886787 0.0599790836859295 0.5515666137698798 chr22 51304566 2722748 0.053070286180766056 0.5550640974903982 chrMT 16571 263486 15.900428459356707 14.216952534240335 chrX 155270560 6899200 0.044433407079874 0.5144784827529586 chrY 59373566 2032601 0.03423410680773326 1.4852196459037559