BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081039.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 = 1,416,911 number of mapped reads = 1,162,400 (82.04%) number of supplementary alignments = 6,370 (0.45%) number of secondary alignments = 0 number of mapped bases = 77,030,783 bp number of sequenced bases = 77,002,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,441 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1284 >>>>>>> ACTG content number of A's = 23,010,681 bp (29.88%) number of C's = 14,557,261 bp (18.9%) number of T's = 22,668,741 bp (29.44%) number of G's = 16,765,213 bp (21.77%) number of N's = 1,043 bp (0%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 637,343 number of insertions = 4,957 mapped reads with insertion percentage = 0.42% number of deletions = 16,330 mapped reads with deletion percentage = 1.39% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2114X There is a 2.29% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 5999677 0.024070860790352856 0.29017656429710453 chr2 243199373 6612144 0.027188162199743827 0.22584275808706789 chr3 198022430 5151730 0.02601589123009954 0.1711668906365995 chr4 191154276 5092422 0.026640377116125824 0.17677243426172898 chr5 180915260 4707122 0.02601838009684755 0.17172198245491016 chr6 171115067 4323112 0.025264356177355205 0.20209999890389777 chr7 159138663 4379337 0.027519000835139605 0.3054511370739551 chr8 146364022 3842749 0.026254737656771963 0.2197947891184738 chr9 141213431 3298483 0.023358139354322464 0.1999531447585599 chr10 135534747 3705381 0.02733897455831013 0.2073325999886395 chr11 135006516 3574165 0.026474018483670817 0.2139292148989183 chr12 133851895 3516536 0.026271843218954802 0.17336591236443605 chr13 115169878 2522077 0.02189875550619234 0.1564977636627844 chr14 107349540 2281396 0.02125203331099509 0.16038889300747167 chr15 102531392 2180678 0.02126839358622967 0.1570735387274711 chr16 90354753 2214763 0.024511859381653116 0.1756783744778579 chr17 81195210 2019185 0.02486827732818229 0.18653866205430397 chr18 78077248 2110773 0.027034418528685846 0.36122611518899633 chr19 59128983 1416465 0.023955510954754625 0.22860287091413442 chr20 63025520 1560902 0.024766189949721955 0.1685587675472142 chr21 48129895 997211 0.020719160097897576 0.16069502999781193 chr22 51304566 832469 0.01622602167612138 0.13467901434109392 chrMT 16571 11203 0.6760605877738217 0.8914754414771897 chrX 155270560 4509925 0.029045589840083014 0.1960076802853092 chrY 59373566 170878 0.0028780147717588664 0.06997418212475262