BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231778.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,676,015 number of mapped reads = 2,366,412 (88.43%) number of supplementary alignments = 16,962 (0.63%) number of secondary alignments = 0 number of mapped bases = 157,751,842 bp number of sequenced bases = 157,688,390 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,059 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5759 >>>>>>> ACTG content number of A's = 44,192,350 bp (28.03%) number of C's = 31,012,885 bp (19.67%) number of T's = 45,370,579 bp (28.77%) number of G's = 37,101,521 bp (23.53%) number of N's = 11,055 bp (0.01%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,001,587 number of insertions = 12,977 mapped reads with insertion percentage = 0.54% number of deletions = 37,580 mapped reads with deletion percentage = 1.57% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 4.6676X There is a 4.39% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15446385 0.06197129996318043 1.2525269395490204 chr2 243199373 12771189 0.052513248050191315 16.545361041940623 chr3 198022430 16023090 0.08091553062953526 0.31303553347764507 chr4 191154276 3523365 0.018432049095255396 0.17118988351149644 chr5 180915260 7821483 0.0432328538786612 0.23486936290593155 chr6 171115067 11851927 0.06926290716410145 0.37516724187295386 chr7 159138663 11904640 0.07480671117615208 0.9206106538738243 chr8 146364022 9543273 0.06520231454147933 0.5511527519661324 chr9 141213431 7476403 0.05294399369136495 0.4064609997037157 chr10 135534747 7327636 0.05406463037851098 0.4547712916919572 chr11 135006516 3974960 0.029442727045856067 0.4577193972366323 chr12 133851895 5831086 0.04356371644943839 0.23640197583700698 chr13 115169878 4887125 0.0424340555435858 0.2238327633879459 chr14 107349540 6077284 0.056612110308064664 0.31181940479077236 chr15 102531392 3178351 0.030998808638041313 0.19789035527658627 chr16 90354753 4584034 0.05073373395199254 0.2933741719379806 chr17 81195210 4471641 0.05507271919119367 0.28547522485838117 chr18 78077248 3210179 0.04111542199848028 0.8464505731887404 chr19 59128983 3980271 0.06731505935084323 0.783505137664712 chr20 63025520 3721512 0.059047700042776326 0.2816782543581266 chr21 48129895 2852008 0.05925647666590588 0.28767523707904413 chr22 51304566 1474057 0.02873149730961568 0.18377079851190087 chrMT 16571 198402 11.972844125279103 7.12125648258023 chrX 155270560 5274379 0.03396895715453078 0.23649407261926703 chrY 59373566 347162 0.005847080163586604 0.12118845127840619