BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082485.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,544,581 number of mapped reads = 1,405,794 (91.01%) number of supplementary alignments = 12,527 (0.81%) number of secondary alignments = 0 number of mapped bases = 97,921,981 bp number of sequenced bases = 97,884,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,820 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5275 >>>>>>> ACTG content number of A's = 29,029,580 bp (29.66%) number of C's = 18,433,008 bp (18.83%) number of T's = 29,935,177 bp (30.58%) number of G's = 20,484,365 bp (20.93%) number of N's = 2,103 bp (0%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 847,075 number of insertions = 8,283 mapped reads with insertion percentage = 0.58% number of deletions = 22,826 mapped reads with deletion percentage = 1.61% homopolymer indels = 46.35% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.3187X There is a 2.87% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 7766398 0.031158991575792303 0.5664609977012085 chr2 243199373 8462632 0.034797096290211244 0.32964989221871893 chr3 198022430 6734553 0.0340090412990084 0.1972119021971567 chr4 191154276 6702643 0.035064049521968316 0.206932958679405 chr5 180915260 6065868 0.03352878026983462 0.1968364339003837 chr6 171115067 5828049 0.0340592392135755 0.2353158354096406 chr7 159138663 5436467 0.03416182401884324 0.3998330777273302 chr8 146364022 5079024 0.03470131478075944 0.5982293301007824 chr9 141213431 4099133 0.02902792582102194 0.27678318146356257 chr10 135534747 4604462 0.03397255760546777 0.2865696131644452 chr11 135006516 4469929 0.03310898712473997 0.2676677971167928 chr12 133851895 4448165 0.033231991224330446 0.19763958237281282 chr13 115169878 3183582 0.02764248825547944 0.17675869660681576 chr14 107349540 2975311 0.027716103860342577 0.1871920672851526 chr15 102531392 2720065 0.026529094621089315 0.1737382290547874 chr16 90354753 2577634 0.02852792923909603 0.2039391461815485 chr17 81195210 2361351 0.029082392914557397 0.20691866818672783 chr18 78077248 2635276 0.03375216298607246 0.4885348439781235 chr19 59128983 1681715 0.02844146668309854 0.4282985322988495 chr20 63025520 1887514 0.02994840820036074 0.18860918831851986 chr21 48129895 1297865 0.026965880561343424 0.18586587583715963 chr22 51304566 953609 0.018587215024877122 0.1441235661440119 chrMT 16571 2872 0.1733148271075976 0.44014358839458595 chrX 155270560 5704685 0.03674028740541671 0.22666312488771376 chrY 59373566 243179 0.004095745234503853 0.10722921353279408