BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082898.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 = 3,227,534 number of mapped reads = 2,700,826 (83.68%) number of supplementary alignments = 17,874 (0.55%) number of secondary alignments = 0 number of mapped bases = 181,373,071 bp number of sequenced bases = 181,305,119 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,631 duplication rate = 4.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7407 >>>>>>> ACTG content number of A's = 50,307,396 bp (27.75%) number of C's = 32,793,171 bp (18.09%) number of T's = 59,187,480 bp (32.65%) number of G's = 39,007,289 bp (21.51%) number of N's = 9,783 bp (0.01%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,603,517 number of insertions = 14,514 mapped reads with insertion percentage = 0.53% number of deletions = 39,817 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.12% >>>>>>> Coverage mean coverageData = 0.0586X std coverageData = 0.4635X There is a 4.72% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16739067 0.06715757390229331 0.8969435164605346 chr2 243199373 15463858 0.06358510636456287 0.5968336139641599 chr3 198022430 15226767 0.07689415284925046 0.3290279017031587 chr4 191154276 8855282 0.046325314742109144 0.2638344933369563 chr5 180915260 11673711 0.0645258503898455 0.30421309981337913 chr6 171115067 11029605 0.06445724034342341 0.48111178840701857 chr7 159138663 9236116 0.058038165118931534 0.4045416138169783 chr8 146364022 17962362 0.12272388907159165 0.6180256075912712 chr9 141213431 5314171 0.03763219236561145 0.4139160797244191 chr10 135534747 7703686 0.0568391956344597 0.37547612352556725 chr11 135006516 7560600 0.05600174142705823 0.37442272064233884 chr12 133851895 5977832 0.04466004758468305 0.25684613104790965 chr13 115169878 4013848 0.03485154338706515 0.2220048017738332 chr14 107349540 3607502 0.03360519290534454 0.23291402273986855 chr15 102531392 3573232 0.03485012668120218 0.2206809241850514 chr16 90354753 5914681 0.06546065152765124 0.33891788113092947 chr17 81195210 4378162 0.05392143206477328 0.3502605164482836 chr18 78077248 6792830 0.0870014014838228 0.7725112007062769 chr19 59128983 2871839 0.048569057918686 0.5649702146264859 chr20 63025520 4044274 0.06416883192713047 0.30679058926833463 chr21 48129895 3014359 0.06262966083761454 0.3046222850593489 chr22 51304566 2367263 0.046141370731018365 0.25132192165164435 chrMT 16571 143369 8.65180133968982 5.750169756277496 chrX 155270560 7597348 0.04892973915982528 0.29997353897375517 chrY 59373566 311307 0.005243191894520872 0.1112501189583497