BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081203.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 = 7,672,424 number of mapped reads = 6,647,895 (86.65%) number of supplementary alignments = 47,661 (0.62%) number of secondary alignments = 0 number of mapped bases = 458,503,942 bp number of sequenced bases = 458,329,231 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 494,335 duplication rate = 5.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9549 >>>>>>> ACTG content number of A's = 135,469,149 bp (29.56%) number of C's = 88,770,859 bp (19.37%) number of T's = 140,516,850 bp (30.66%) number of G's = 93,312,340 bp (20.36%) number of N's = 260,033 bp (0.06%) GC percentage = 39.73% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 4,628,605 number of insertions = 34,790 mapped reads with insertion percentage = 0.52% number of deletions = 108,929 mapped reads with deletion percentage = 1.62% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.1481X std coverageData = 1.6806X There is a 8.42% of reference with a coverageData >= 1X There is a 3.48% of reference with a coverageData >= 2X There is a 1.47% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.02% 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% 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 49134793 0.19713007254653941 4.0614778486433725 chr2 243199373 27279254 0.1121682743812008 1.1442727580675116 chr3 198022430 28175910 0.14228645714528398 0.5995348781500061 chr4 191154276 23824285 0.12463380625605257 0.5968469638095041 chr5 180915260 31704507 0.17524506777371904 0.6703140754328134 chr6 171115067 29953916 0.17505130626515783 0.9536079534387385 chr7 159138663 28299231 0.17782750254725968 2.4285359178250703 chr8 146364022 26814338 0.18320306885253537 2.79575547935829 chr9 141213431 22198490 0.15719814923270295 1.1476553009905812 chr10 135534747 14437561 0.10652294942491758 1.476556522604723 chr11 135006516 23096214 0.1710748094558636 1.3449298385215807 chr12 133851895 11936697 0.0891783937761957 0.5056250298950931 chr13 115169878 13516871 0.11736463765291129 0.5185187994651366 chr14 107349540 16220113 0.1510962506220334 0.6975002873199887 chr15 102531392 15623339 0.15237615227149165 0.5884166673560606 chr16 90354753 14133891 0.15642664642113516 0.7221155634130008 chr17 81195210 7313644 0.09007482091615995 0.5774051169895931 chr18 78077248 13859522 0.1775103804888205 2.159287126007198 chr19 59128983 9779038 0.16538485026877597 2.4413586396058804 chr20 63025520 11871734 0.18836391988515128 0.6917188990891181 chr21 48129895 6942328 0.14424149481315096 0.6875492283641684 chr22 51304566 3216338 0.06269106730188498 0.3611348546807131 chrMT 16571 194600 11.743407157081649 8.493403498190427 chrX 155270560 27929205 0.17987443981653703 0.8380448410715655 chrY 59373566 1048123 0.01765302424314551 0.38778729083943236