BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240012.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 = 886,074 number of mapped reads = 707,899 (79.89%) number of supplementary alignments = 2,900 (0.33%) number of secondary alignments = 0 number of mapped bases = 43,084,059 bp number of sequenced bases = 43,060,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,704 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2205 >>>>>>> ACTG content number of A's = 11,795,297 bp (27.39%) number of C's = 7,249,122 bp (16.83%) number of T's = 13,856,128 bp (32.18%) number of G's = 10,133,021 bp (23.53%) number of N's = 27,212 bp (0.06%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 421,983 number of insertions = 2,953 mapped reads with insertion percentage = 0.41% number of deletions = 13,702 mapped reads with deletion percentage = 1.92% homopolymer indels = 49.31% >>>>>>> Coverage mean coverageData = 0.0139X std coverageData = 0.1588X There is a 1.26% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5550906 0.022270379819836036 0.23491171942687716 chr2 243199373 3629071 0.014922205412100301 0.17266756734531924 chr3 198022430 3680765 0.018587616564446765 0.14875931404788065 chr4 191154276 3517068 0.01839910711701788 0.14906268574281925 chr5 180915260 2027409 0.011206401273170654 0.11577233538304409 chr6 171115067 2180075 0.01274040350871031 0.1325559001267664 chr7 159138663 2467165 0.015503240717813496 0.263881043032492 chr8 146364022 2229287 0.015231113285476673 0.20540532325852678 chr9 141213431 1656925 0.011733480223988043 0.1370317963641638 chr10 135534747 1425309 0.010516188885496647 0.1210076173056636 chr11 135006516 1506585 0.011159350264249468 0.12829197259976025 chr12 133851895 1476223 0.011028779233943607 0.11547570246486841 chr13 115169878 1122331 0.009745004679088051 0.10640552163033005 chr14 107349540 1585612 0.01477055234703381 0.1347937201024405 chr15 102531392 808475 0.007885146043857476 0.10419148095654299 chr16 90354753 1090493 0.012069016446760693 0.1217041979697521 chr17 81195210 1062790 0.013089318938888143 0.12708680450315193 chr18 78077248 1618638 0.02073123786330174 0.21506078411957294 chr19 59128983 652939 0.011042621856019407 0.16220183553414316 chr20 63025520 705490 0.011193719623416039 0.11815295127226956 chr21 48129895 741560 0.015407471801050053 0.13594299858858236 chr22 51304566 298809 0.005824218452603225 0.08300896925798003 chrMT 16571 24950 1.50564238730312 1.9525216830316925 chrX 155270560 1936618 0.012472538258379438 0.12842936712762884 chrY 59373566 88566 0.0014916739210173093 0.043808537828217586