BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237834.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 = 2,775,833 number of mapped reads = 2,180,493 (78.55%) number of supplementary alignments = 11,626 (0.42%) number of secondary alignments = 0 number of mapped bases = 139,471,401 bp number of sequenced bases = 139,402,579 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,983 duplication rate = 7.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.13 >>>>>>> ACTG content number of A's = 38,836,038 bp (27.86%) number of C's = 25,259,904 bp (18.12%) number of T's = 44,469,204 bp (31.9%) number of G's = 30,728,032 bp (22.04%) number of N's = 109,401 bp (0.08%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,138,997 number of insertions = 11,706 mapped reads with insertion percentage = 0.53% number of deletions = 42,526 mapped reads with deletion percentage = 1.93% homopolymer indels = 48.32% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.4039X There is a 2.88% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% 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 16295383 0.0653775021086106 0.5429700039327666 chr2 243199373 13390913 0.05506146185664714 0.4362196699425101 chr3 198022430 9004136 0.04547028334113464 0.3350262500421657 chr4 191154276 11022316 0.05766188562792077 0.37048208342613104 chr5 180915260 10622475 0.058715196274764216 0.35693557445314916 chr6 171115067 7024628 0.04105207170330594 0.3324222530013401 chr7 159138663 8109091 0.050956133771213094 0.41444103149124834 chr8 146364022 5546785 0.03789718896902136 0.3847432809281266 chr9 141213431 4174906 0.029564510758187015 0.3397709760637027 chr10 135534747 5039947 0.03718564509512826 0.7646603566519816 chr11 135006516 4137251 0.030644824580170635 0.31716081362494086 chr12 133851895 8292870 0.06195556663579548 0.36759236889371444 chr13 115169878 3241033 0.028141325286460753 0.2499849535733809 chr14 107349540 4907729 0.04571728020446105 0.3240201422501937 chr15 102531392 3192112 0.03113302119218278 0.26250854876351504 chr16 90354753 2599696 0.028772100124052135 0.2803531926863951 chr17 81195210 3365856 0.041453873941578574 0.3067749548429748 chr18 78077248 5042948 0.06458921298045751 0.7104993018372536 chr19 59128983 1739805 0.029423895215650843 0.3533656637940617 chr20 63025520 3820451 0.06061752445675974 0.36531718101361466 chr21 48129895 1362032 0.02829908521512461 0.2657250607919309 chr22 51304566 924429 0.018018454731689962 0.19043866696245773 chrMT 16571 38013 2.293947257256653 2.731057499191647 chrX 155270560 6115941 0.03938892859019765 0.3151343257050845 chrY 59373566 460655 0.00775858738213568 0.16541486753615658