BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083673.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 = 1,603,311 number of mapped reads = 1,425,897 (88.93%) number of supplementary alignments = 11,499 (0.72%) number of secondary alignments = 0 number of mapped bases = 93,738,606 bp number of sequenced bases = 93,703,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,736 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1763 >>>>>>> ACTG content number of A's = 24,573,009 bp (26.22%) number of C's = 17,445,617 bp (18.62%) number of T's = 29,575,291 bp (31.56%) number of G's = 22,105,317 bp (23.59%) number of N's = 4,478 bp (0%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 667,973 number of insertions = 7,161 mapped reads with insertion percentage = 0.5% number of deletions = 21,396 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.77% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.2614X There is a 2.56% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 9067400 0.03637864557216088 0.4061817351444853 chr2 243199373 7353464 0.03023636084785465 0.4013790494685068 chr3 198022430 6224969 0.03143567625142263 0.20592223620260797 chr4 191154276 4805389 0.025138799406192725 0.18668820428543056 chr5 180915260 5076687 0.028061132046019777 0.1932416709307451 chr6 171115067 6301056 0.03682350193042907 0.26339283997278 chr7 159138663 5802402 0.03646129664919957 0.3018894004617671 chr8 146364022 5138312 0.035106387005407656 0.2475604654042467 chr9 141213431 4281233 0.030317463216370688 0.23544594901758484 chr10 135534747 4658369 0.03437029325033528 0.2383040703507082 chr11 135006516 3482378 0.02579414759506867 0.21285274488210848 chr12 133851895 3920795 0.02929203953369506 0.19700844380866608 chr13 115169878 3117776 0.02707110621407448 0.19046290042839753 chr14 107349540 1798354 0.01675232143519199 0.1523750295192449 chr15 102531392 2513797 0.024517340016216693 0.19049368754168475 chr16 90354753 2845159 0.03148875853824757 0.21246576556890753 chr17 81195210 2572811 0.031686733737125626 0.2109821589088407 chr18 78077248 2430112 0.031124457665311155 0.35506163923388434 chr19 59128983 2629972 0.04447855969381378 0.3064172396961097 chr20 63025520 2496632 0.03961303294284601 0.2320091480695642 chr21 48129895 1997209 0.04149622599425991 0.24210206434471102 chr22 51304566 928205 0.018092054418704175 0.15402401526646275 chrMT 16571 2503 0.1510470098364613 0.4195547046151499 chrX 155270560 4111411 0.026479011861617552 0.194901445029291 chrY 59373566 182211 0.0030688909606675805 0.07463558055138496