BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716967.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,781,075 number of mapped reads = 1,345,363 (75.54%) number of supplementary alignments = 4,625 (0.26%) number of secondary alignments = 0 number of mapped bases = 72,423,482 bp number of sequenced bases = 72,403,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,990 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.1596 >>>>>>> ACTG content number of A's = 17,368,110 bp (23.99%) number of C's = 15,083,366 bp (20.83%) number of T's = 20,799,147 bp (28.73%) number of G's = 19,151,281 bp (26.45%) number of N's = 1,888 bp (0%) GC percentage = 47.28% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 387,105 number of insertions = 7,437 mapped reads with insertion percentage = 0.55% number of deletions = 12,128 mapped reads with deletion percentage = 0.89% homopolymer indels = 31% >>>>>>> Coverage mean coverageData = 0.0234X std coverageData = 0.1957X There is a 2.1% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6643645 0.026654477221944414 0.23245609658023092 chr2 243199373 6057820 0.02490886356026913 0.23758236704865757 chr3 198022430 4985350 0.02517568338091801 0.18243368154106798 chr4 191154276 4722312 0.024704192335200496 0.192797486981866 chr5 180915260 4431472 0.02449473858645202 0.1720382740859772 chr6 171115067 3066811 0.017922507081156096 0.15407540612299092 chr7 159138663 4259494 0.026765928025925416 0.2281450507466772 chr8 146364022 3776935 0.025805077971962263 0.18880244001451638 chr9 141213431 3194066 0.022618712521757227 0.17945783343717928 chr10 135534747 3904031 0.028804650367628606 0.24762243872442039 chr11 135006516 3041270 0.022526838630514693 0.20834455485652872 chr12 133851895 3608122 0.02695607708803824 0.18228893320694142 chr13 115169878 1308505 0.011361521108844103 0.11901178321265957 chr14 107349540 2369368 0.022071524479750915 0.16986890286570933 chr15 102531392 1501164 0.014641018430726075 0.13915193734293743 chr16 90354753 2037890 0.02255431985963151 0.17962599602922674 chr17 81195210 3056935 0.03764920369071033 0.2291575740249218 chr18 78077248 1978980 0.025346436390790823 0.22485969432603084 chr19 59128983 2091759 0.035376204593270275 0.24473198673773625 chr20 63025520 1908071 0.030274577663143436 0.19799707103055614 chr21 48129895 993649 0.020645152041158618 0.17238931731894724 chr22 51304566 857988 0.016723423798185914 0.14443059867434657 chrMT 16571 99546 6.007241566592239 5.353353282956072 chrX 155270560 2318762 0.014933687364816614 0.14815857244325273 chrY 59373566 209537 0.003529129444574712 0.102720583939528