BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237285.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,348,509 number of mapped reads = 407,174 (12.16%) number of supplementary alignments = 3,313 (0.1%) number of secondary alignments = 0 number of mapped bases = 25,454,480 bp number of sequenced bases = 25,439,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,588 duplication rate = 8.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5951 >>>>>>> ACTG content number of A's = 6,694,368 bp (26.32%) number of C's = 4,428,579 bp (17.41%) number of T's = 8,414,532 bp (33.08%) number of G's = 5,899,216 bp (23.19%) number of N's = 2,619 bp (0.01%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 178,151 number of insertions = 2,355 mapped reads with insertion percentage = 0.57% number of deletions = 8,343 mapped reads with deletion percentage = 2.02% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.0082X std coverageData = 0.154X There is a 0.66% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 1662387 0.006669540053021573 0.16107659148286582 chr2 243199373 1770531 0.007280162683643103 0.23037468581806636 chr3 198022430 1693658 0.008552859390726596 0.11110525360513916 chr4 191154276 1630012 0.008527206579464642 0.15014006404454214 chr5 180915260 1388577 0.007675289525051673 0.10505972193715186 chr6 171115067 1654961 0.009671626403302054 0.1266994285004384 chr7 159138663 1134165 0.0071268978802467384 0.1228731150129088 chr8 146364022 1596177 0.010905528409160552 0.30449463747700584 chr9 141213431 1392849 0.009863431474871537 0.13458696172434076 chr10 135534747 1823911 0.013457146896802781 0.2096739908269715 chr11 135006516 1040240 0.00770510958152568 0.1147393853687228 chr12 133851895 1240797 0.009269924792622473 0.11694537751084703 chr13 115169878 1031810 0.008959026595478377 0.11805830211606948 chr14 107349540 739050 0.006884519486529705 0.10011830641385908 chr15 102531392 461150 0.004497646925538668 0.07967166051926182 chr16 90354753 782913 0.008664878979858426 0.11934214165955867 chr17 81195210 724511 0.008923075634634112 0.12060454599822802 chr18 78077248 737849 0.009450243430711082 0.19499688734529408 chr19 59128983 445544 0.00753512029794255 0.1374564549430168 chr20 63025520 493481 0.007829860031301606 0.11297898816126326 chr21 48129895 384593 0.00799073008573985 0.1228219937067963 chr22 51304566 236148 0.004602865171883532 0.08027341316465687 chrMT 16571 17967 1.0842435580230523 1.3603260141995797 chrX 155270560 1255009 0.008082723473142622 0.11189168797359096 chrY 59373566 116190 0.001956931473511293 0.1109179937902337