BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548989.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,351,606 number of mapped reads = 8,062,584 (86.22%) number of secondary alignments = 0 number of mapped bases = 318,456,327 bp number of sequenced bases = 318,422,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 745,011 duplication rate = 6.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.3082 >>>>>>> ACTG content number of A's = 94,601,382 bp (29.71%) number of C's = 64,563,799 bp (20.28%) number of T's = 94,538,449 bp (29.69%) number of G's = 64,715,789 bp (20.32%) number of N's = 2,888 bp (0%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,268,443 number of insertions = 12,926 mapped reads with insertion percentage = 0.16% number of deletions = 27,251 mapped reads with deletion percentage = 0.34% homopolymer indels = 39.48% >>>>>>> Coverage mean coverageData = 0.1029X std coverageData = 1.3225X There is a 8.11% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 25103989 0.10071785939502233 2.310802802535296 chr2 243199373 28078083 0.11545294156658865 1.3861630704053565 chr3 198022430 21523500 0.10869223249103649 0.4150678670725685 chr4 191154276 22325029 0.11679063355088118 0.5644477271091902 chr5 180915260 20198338 0.11164529736186986 0.4785529444478221 chr6 171115067 18857365 0.11020283210946001 0.565635481328781 chr7 159138663 18728399 0.11768603962696356 1.7729237046062571 chr8 146364022 16708238 0.11415536257947326 2.5545602489565056 chr9 141213431 13797963 0.09770999048950238 1.3489584895465943 chr10 135534747 15491200 0.11429688949063371 1.150238052922556 chr11 135006516 14796302 0.10959694715772089 0.9378767756742639 chr12 133851895 14480190 0.10818068731862182 0.5287567563856884 chr13 115169878 10467524 0.09088768853258662 0.3491716436457696 chr14 107349540 9607006 0.08949275423071212 0.7747095530264996 chr15 102531392 8597172 0.08384916884772227 0.35468042702834796 chr16 90354753 8257407 0.0913887396715035 0.6374401582309533 chr17 81195210 7595209 0.09354257474055427 0.47712109989056767 chr18 78077248 8822792 0.1130008065858059 3.073386204556878 chr19 59128983 6199961 0.10485485603566021 2.283404096589281 chr20 63025520 6090536 0.09663602934176505 0.5373756499859768 chr21 48129895 4102559 0.08523930916533269 0.7416302721319571 chr22 51304566 3076418 0.05996382466231173 0.3240975575204405 chrMT 16571 8947 0.53991913583972 0.9457744706070952 chrX 155270560 12315537 0.07931662641005481 0.839124724658308 chrY 59373566 3226663 0.054345110414961435 0.6412500840532452