BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819151.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 = 21,337,406 number of mapped reads = 20,898,728 (97.94%) number of supplementary alignments = 10,546 (0.05%) number of secondary alignments = 0 number of mapped bases = 1,417,747,136 bp number of sequenced bases = 1,417,513,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,118,721 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7925 >>>>>>> ACTG content number of A's = 401,208,997 bp (28.3%) number of C's = 297,799,518 bp (21.01%) number of T's = 417,007,026 bp (29.42%) number of G's = 301,408,441 bp (21.26%) number of N's = 89,184 bp (0.01%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 4,180,589 number of insertions = 111,654 mapped reads with insertion percentage = 0.53% number of deletions = 113,223 mapped reads with deletion percentage = 0.54% homopolymer indels = 36.64% >>>>>>> Coverage mean coverageData = 0.458X std coverageData = 4.9285X There is a 32.12% of reference with a coverageData >= 1X There is a 8.27% of reference with a coverageData >= 2X There is a 2.1% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% 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 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 132187435 0.5303394409597078 7.762434740635154 chr2 243199373 101450925 0.4171512605009882 3.3925764777065543 chr3 198022430 86175821 0.4351821205304874 2.8036403009712076 chr4 191154276 73378670 0.38387145469871675 2.8904918131910997 chr5 180915260 65794311 0.36367474473960903 0.7212555937525663 chr6 171115067 68229670 0.3987356063741599 1.2129476996629407 chr7 159138663 122638163 0.77063713297629 6.867103158817922 chr8 146364022 125450124 0.8571103901476552 2.5027994789736474 chr9 141213431 50619269 0.35845930972387463 1.8728659905089642 chr10 135534747 74926119 0.5528185255696829 16.442079051246083 chr11 135006516 61457463 0.45521849478731824 1.8976938607153424 chr12 133851895 54300430 0.40567546690317685 0.7867148031669511 chr13 115169878 41274522 0.35837948877570225 0.65453313834405 chr14 107349540 42832878 0.39900383364474595 0.8758795039043837 chr15 102531392 38281584 0.37336452039976203 0.6771920671741957 chr16 90354753 40769973 0.45122112170457707 5.091526304931783 chr17 81195210 38655294 0.4760785026604402 1.8755054031512548 chr18 78077248 25758638 0.32991221719290104 3.8817825647771995 chr19 59128983 25695762 0.43457135056762264 4.919744847475614 chr20 63025520 57866789 0.9181485372909259 1.446163233009026 chr21 48129895 14970215 0.3110377656132431 2.664604955063062 chr22 51304566 15232377 0.29690100097523486 0.8399278428693819 chrMT 16571 1350461 81.49544384768572 25.66521482122502 chrX 155270560 52663648 0.33917342733870476 1.1400922857074445 chrY 59373566 5786595 0.09746079593737052 4.906779714302405