BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236079.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 = 1,403,393 number of mapped reads = 1,207,104 (86.01%) number of supplementary alignments = 11,630 (0.83%) number of secondary alignments = 0 number of mapped bases = 75,543,323 bp number of sequenced bases = 75,505,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,823 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4044 >>>>>>> ACTG content number of A's = 21,220,353 bp (28.1%) number of C's = 13,930,329 bp (18.45%) number of T's = 23,893,287 bp (31.64%) number of G's = 16,421,855 bp (21.75%) number of N's = 40,025 bp (0.05%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 742,221 number of insertions = 5,676 mapped reads with insertion percentage = 0.47% number of deletions = 21,727 mapped reads with deletion percentage = 1.78% homopolymer indels = 44.87% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2309X There is a 2% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 7245910 0.029070780128567866 0.3133793024301337 chr2 243199373 2770810 0.01139316259668153 0.22774624636460183 chr3 198022430 10110120 0.05105542841788175 0.2676994304612819 chr4 191154276 4747669 0.024836844350790248 0.1896551290067997 chr5 180915260 4964806 0.027442715445894394 0.19554282926395153 chr6 171115067 9765374 0.057069048162778094 0.33258416836781524 chr7 159138663 1612371 0.010131862173556152 0.19452872486634384 chr8 146364022 6641579 0.04537712826721856 0.40396764053417056 chr9 141213431 2764655 0.019577847379120758 0.1863125521921466 chr10 135534747 2197974 0.01621705170556743 0.1999174558966019 chr11 135006516 718123 0.005319172890884763 0.10957932568751437 chr12 133851895 2764547 0.02065377557785043 0.1709294506274064 chr13 115169878 2966870 0.02576081568828266 0.1949603747740571 chr14 107349540 1387175 0.012922039535521065 0.13915538218964996 chr15 102531392 293401 0.002861572385557781 0.07188160067770814 chr16 90354753 2268130 0.025102497928360227 0.19167955713023127 chr17 81195210 1545522 0.019034645024010654 0.16576671977963275 chr18 78077248 839819 0.010756257700066477 0.25950196687462795 chr19 59128983 1078604 0.018241544928990237 0.24352961881401225 chr20 63025520 1897110 0.030100663985001632 0.2054333222329871 chr21 48129895 1339209 0.027824889291780088 0.1988231442486048 chr22 51304566 943130 0.018382964198547163 0.15668215591221119 chrMT 16571 66116 3.9898618067708647 3.3845172617236168 chrX 155270560 4422882 0.0284850006337325 0.20875050868393344 chrY 59373566 191417 0.0032239431264748358 0.07532239055997451