BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231876.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 = 2,035,739 number of mapped reads = 694,826 (34.13%) number of supplementary alignments = 4,823 (0.24%) number of secondary alignments = 0 number of mapped bases = 42,821,646 bp number of sequenced bases = 42,797,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,556 duplication rate = 14.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6196 >>>>>>> ACTG content number of A's = 11,471,266 bp (26.8%) number of C's = 7,129,645 bp (16.66%) number of T's = 14,503,836 bp (33.89%) number of G's = 9,682,813 bp (22.62%) number of N's = 10,434 bp (0.02%) GC percentage = 39.28% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 399,483 number of insertions = 4,450 mapped reads with insertion percentage = 0.63% number of deletions = 14,414 mapped reads with deletion percentage = 2.05% homopolymer indels = 45.79% >>>>>>> Coverage mean coverageData = 0.0138X std coverageData = 0.2334X There is a 0.71% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% 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 2799969 0.011233548742091199 0.2343418521608656 chr2 243199373 4896565 0.02013395404600817 0.3115622743020207 chr3 198022430 3166596 0.015991097574148544 0.22422259289266339 chr4 191154276 2109395 0.011035039571911015 0.1958654376105931 chr5 180915260 2183436 0.012068832667846814 0.1948659486609458 chr6 171115067 1948340 0.011386139363168995 0.20762246632991369 chr7 159138663 2133721 0.013407935945773278 0.23632457988886482 chr8 146364022 2345044 0.016021997537072327 0.3451913135881338 chr9 141213431 1393538 0.009868310614165305 0.18116342764716994 chr10 135534747 3886817 0.028677642346578474 0.30981674097281636 chr11 135006516 1610210 0.01192690580949441 0.19883111954978036 chr12 133851895 1548650 0.01156987728862561 0.18866299827695993 chr13 115169878 1047302 0.009093540934375218 0.20002358430241446 chr14 107349540 1362808 0.01269505207008805 0.20512905669437148 chr15 102531392 1028106 0.01002723146487663 0.17595349091834334 chr16 90354753 1626275 0.017998776445108538 0.23355552757473722 chr17 81195210 870655 0.010722984767204864 0.17846682020964416 chr18 78077248 1652182 0.02116086366158807 0.3416896127460269 chr19 59128983 551568 0.00932821726360489 0.17671332775894785 chr20 63025520 716369 0.011366332241288926 0.18562790340832805 chr21 48129895 1187810 0.024679256000870144 0.2903213079338367 chr22 51304566 345575 0.006735755254220453 0.1343970527515378 chrMT 16571 39567 2.387725544626154 3.2033898660563125 chrX 155270560 2244938 0.014458233421712397 0.2134497466574342 chrY 59373566 126210 0.0021256934441161914 0.07352740618525833