BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085120.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 = 2,213,323 number of mapped reads = 2,000,799 (90.4%) number of supplementary alignments = 19,350 (0.87%) number of secondary alignments = 0 number of mapped bases = 135,106,429 bp number of sequenced bases = 135,058,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,651 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3071 >>>>>>> ACTG content number of A's = 37,958,859 bp (28.11%) number of C's = 25,206,908 bp (18.66%) number of T's = 42,205,222 bp (31.25%) number of G's = 29,655,535 bp (21.96%) number of N's = 31,630 bp (0.02%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,159,063 number of insertions = 10,531 mapped reads with insertion percentage = 0.52% number of deletions = 29,930 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.3565X There is a 3.86% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 10908753 0.04376620189042578 0.5852265327262246 chr2 243199373 11848919 0.048721009654905646 0.4343906409210735 chr3 198022430 9249774 0.0467107387784303 0.23615841266402943 chr4 191154276 8987967 0.047019439941798635 0.24439524304883542 chr5 180915260 8579251 0.04742137838455418 0.23957510772478907 chr6 171115067 8195787 0.04789634918589606 0.2836028336916354 chr7 159138663 7608780 0.047812265458080414 0.4852635205939438 chr8 146364022 6953558 0.04750865619147853 0.6113130427703094 chr9 141213431 5756578 0.040765088414288296 0.32227776793532126 chr10 135534747 5701003 0.042063036425633346 0.31248266200932784 chr11 135006516 5921226 0.043858816414461065 0.2900687197122344 chr12 133851895 6051269 0.04520869129271573 0.23533225554554307 chr13 115169878 4360823 0.03786426690492804 0.21453178499701075 chr14 107349540 4120283 0.038381934379970326 0.2279502751829528 chr15 102531392 3787383 0.03693876505646193 0.21595465379779483 chr16 90354753 3612126 0.039977155379972096 0.23798290105563427 chr17 81195210 3300128 0.040644368060628204 0.23721202410154713 chr18 78077248 3616001 0.04631312056490516 0.5056849837939225 chr19 59128983 2403977 0.040656491588904886 0.4354610257777093 chr20 63025520 2588294 0.04106739619125713 0.2262530161569794 chr21 48129895 1779426 0.036971325202350844 0.22157651375449872 chr22 51304566 1316102 0.0256527265039139 0.17399008358384765 chrMT 16571 12585 0.7594592963611128 0.9237516638003364 chrX 155270560 8125296 0.05232992010848676 0.27899442538744035 chrY 59373566 321140 0.00540880431537496 0.1126272945195834