BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003985.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 = 4,306,422 number of mapped reads = 3,646,966 (84.69%) number of supplementary alignments = 28,046 (0.65%) number of secondary alignments = 0 number of mapped bases = 244,180,534 bp number of sequenced bases = 244,069,003 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 325,443 duplication rate = 7.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1201 >>>>>>> ACTG content number of A's = 68,543,429 bp (28.08%) number of C's = 43,400,198 bp (17.78%) number of T's = 81,223,026 bp (33.28%) number of G's = 50,875,519 bp (20.84%) number of N's = 26,831 bp (0.01%) GC percentage = 38.63% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 2,415,142 number of insertions = 21,899 mapped reads with insertion percentage = 0.6% number of deletions = 68,427 mapped reads with deletion percentage = 1.85% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.0789X std coverageData = 0.6596X There is a 5.22% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 14004591 0.056186784786385745 0.9653602477760019 chr2 243199373 16871295 0.06937228000172517 0.8415129832850367 chr3 198022430 22855057 0.11541650609983929 0.47804184112994685 chr4 191154276 13183687 0.06896883122823787 0.38544517077762236 chr5 180915260 18577459 0.10268597021611112 0.457653289977998 chr6 171115067 17547394 0.10254733442029391 0.5140041862173682 chr7 159138663 13235331 0.08316854465467012 0.6937079048675502 chr8 146364022 12208301 0.08341053240529288 1.2457491191373373 chr9 141213431 8078032 0.0572044170501034 0.5916482382255975 chr10 135534747 11315660 0.08348899636784654 0.574877469294787 chr11 135006516 15896789 0.11774830927419828 0.7605464224877744 chr12 133851895 14742419 0.11013978546960429 0.4782156164330722 chr13 115169878 1284614 0.01115407971518386 0.15388237614316413 chr14 107349540 7468392 0.06957078716872005 0.4049055816586955 chr15 102531392 3193437 0.03114594406364833 0.24406086563367582 chr16 90354753 3987525 0.04413187870703382 0.32595062159290583 chr17 81195210 9027252 0.11117961268897512 0.531564797125048 chr18 78077248 6207557 0.07950532529015367 1.004497302056843 chr19 59128983 4795862 0.08110848109800908 0.7078644629189275 chr20 63025520 7482584 0.11872308233236314 0.4974704218997066 chr21 48129895 2882266 0.059885150383145444 0.36365682211004785 chr22 51304566 1185902 0.023114940685786133 0.19700630244681572 chrMT 16571 690137 41.64727536056967 25.210057346667682 chrX 155270560 16960644 0.10923283847240585 0.5337274034571197 chrY 59373566 498347 0.00839341534581231 0.15877036185302235