BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819006.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 = 1,287,925 number of mapped reads = 1,205,555 (93.6%) number of supplementary alignments = 19,427 (1.51%) number of secondary alignments = 0 number of mapped bases = 111,312,892 bp number of sequenced bases = 111,243,122 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,655 duplication rate = 27.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0785 >>>>>>> ACTG content number of A's = 32,691,559 bp (29.39%) number of C's = 23,435,696 bp (21.07%) number of T's = 32,102,551 bp (28.86%) number of G's = 23,007,710 bp (20.68%) number of N's = 5,606 bp (0.01%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 745,969 number of insertions = 19,596 mapped reads with insertion percentage = 1.58% number of deletions = 36,812 mapped reads with deletion percentage = 2.99% homopolymer indels = 41.11% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.4978X There is a 2.15% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 11304268 0.04535301839829719 0.9088385898913681 chr2 243199373 8906848 0.036623647051919006 0.7523531145521526 chr3 198022430 5821356 0.029397457651640778 0.26124565071075345 chr4 191154276 6240296 0.03264533826070414 0.34223706343368226 chr5 180915260 6078091 0.03359634228754391 0.29736375827274386 chr6 171115067 4708063 0.027514017804171505 0.30250621508159414 chr7 159138663 5240142 0.03292815147001706 0.5788707461237707 chr8 146364022 10374367 0.07088058156805775 0.45384143996206117 chr9 141213431 4721055 0.03343205364084667 0.42701088338068793 chr10 135534747 6033441 0.0445158244180734 0.6312619680497276 chr11 135006516 3894503 0.028846778032550667 0.3197506709563517 chr12 133851895 4947149 0.0369598727010925 0.2988882040993898 chr13 115169878 2479933 0.021532826491315726 0.22173784770910282 chr14 107349540 2705250 0.025200387444603862 0.26248270631575754 chr15 102531392 2794639 0.02725642308650213 0.25186424969941235 chr16 90354753 3648262 0.04037709006852135 0.576065000079761 chr17 81195210 3875938 0.04773604255719026 0.36777345158307356 chr18 78077248 2829447 0.036239071848434 0.527146941958461 chr19 59128983 2218948 0.03752724784730358 0.7183178346447304 chr20 63025520 2888706 0.045833909819387446 0.34843407761440237 chr21 48129895 1551543 0.03223657562519096 0.29834108986829005 chr22 51304566 889838 0.017344226242942976 0.21859810485318215 chrMT 16571 124580 7.517953050509927 5.834130970986813 chrX 155270560 6567363 0.042296253713517876 0.37614166923018744 chrY 59373566 468866 0.0078968812484667 0.5210677827284543