BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080812.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 = 2,688,996 number of mapped reads = 2,167,609 (80.61%) number of supplementary alignments = 24,246 (0.9%) number of secondary alignments = 0 number of mapped bases = 147,765,407 bp number of sequenced bases = 147,712,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 178,796 duplication rate = 6.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9105 >>>>>>> ACTG content number of A's = 43,053,287 bp (29.15%) number of C's = 27,188,029 bp (18.41%) number of T's = 46,114,243 bp (31.22%) number of G's = 31,336,814 bp (21.21%) number of N's = 20,035 bp (0.01%) GC percentage = 39.62% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,167,798 number of insertions = 11,019 mapped reads with insertion percentage = 0.5% number of deletions = 30,313 mapped reads with deletion percentage = 1.38% homopolymer indels = 47.92% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.3941X There is a 3.02% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% 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% 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 12527069 0.05025892794064493 0.4417285400576223 chr2 243199373 13196323 0.05426133643856064 0.42917487209881955 chr3 198022430 11729452 0.05923294648995066 0.35483332687763136 chr4 191154276 9757748 0.05104645422632345 0.33437636705241586 chr5 180915260 8880574 0.04908692611115281 0.32068709491992897 chr6 171115067 8833379 0.05162245005578615 0.3465164293757919 chr7 159138663 8176609 0.05138040527586939 0.39987652808439134 chr8 146364022 8853066 0.06048662696629094 0.8715042201377374 chr9 141213431 6079232 0.04304995606260711 0.33994794376225834 chr10 135534747 6325867 0.046673396601389604 0.3514961484992663 chr11 135006516 6210540 0.04600177964743568 0.328104980090021 chr12 133851895 6471079 0.04834506825622454 0.31900768839369253 chr13 115169878 4830131 0.04193918656404238 0.3023925349731952 chr14 107349540 4254497 0.039632186593440456 0.2960519806572428 chr15 102531392 3710344 0.036187395173567914 0.2782506162617277 chr16 90354753 3536102 0.0391357607939009 0.2900458531493223 chr17 81195210 3130225 0.03855184314444165 0.2840866683723631 chr18 78077248 3894162 0.049875758940683974 0.4913256077937425 chr19 59128983 2108760 0.03566372856438271 0.3280197439340328 chr20 63025520 2544289 0.040369186957917996 0.29297874298155574 chr21 48129895 1896436 0.039402454545142886 0.29897870861127845 chr22 51304566 1270307 0.024760115892998685 0.22351249782769214 chrMT 16571 214677 12.954981594351578 7.924978119572496 chrX 155270560 9001508 0.05797305039667532 0.3551076925707492 chrY 59373566 333031 0.005609078625999995 0.12477782930427753