BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063587.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 = 2,712,621 number of mapped reads = 2,219,806 (81.83%) number of supplementary alignments = 25,126 (0.93%) number of secondary alignments = 0 number of mapped bases = 147,659,877 bp number of sequenced bases = 147,601,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 450,856 duplication rate = 12.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7092 >>>>>>> ACTG content number of A's = 41,996,908 bp (28.45%) number of C's = 27,426,511 bp (18.58%) number of T's = 46,747,357 bp (31.67%) number of G's = 31,427,530 bp (21.29%) number of N's = 3,680 bp (0%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,196,170 number of insertions = 12,486 mapped reads with insertion percentage = 0.56% number of deletions = 35,489 mapped reads with deletion percentage = 1.58% homopolymer indels = 46.89% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.7846X There is a 1.39% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 18168035 0.07289063083216953 1.466046209052969 chr2 243199373 5729956 0.023560735084625403 0.8217933635041639 chr3 198022430 4159238 0.021003873147097528 0.3588181961135533 chr4 191154276 5396442 0.02823082021978938 0.4915396274995544 chr5 180915260 4465726 0.024684075848549206 0.38237271941576206 chr6 171115067 21559866 0.12599630399583692 0.9234796177776086 chr7 159138663 7976032 0.050120013890024954 0.6319896671830801 chr8 146364022 3160381 0.021592608325562413 1.0840245332991252 chr9 141213431 5185858 0.03672354650174883 0.650139181879506 chr10 135534747 2704150 0.01995171024298293 0.4749227920968355 chr11 135006516 2844630 0.02107031633939802 0.5527291947361135 chr12 133851895 7059363 0.05274010502428823 0.5812040343065635 chr13 115169878 8133042 0.07061778775175918 0.6814542774881709 chr14 107349540 17377102 0.16187402386633423 1.0703618883348707 chr15 102531392 9396475 0.09164485936170651 0.8264446404599962 chr16 90354753 5883969 0.06512074688533541 0.6688643490860523 chr17 81195210 1452004 0.017882877573689383 0.3114291899322323 chr18 78077248 1863847 0.02387183267525003 1.2609429183610459 chr19 59128983 1352034 0.0228658422892205 0.7755513184101447 chr20 63025520 8411859 0.1334675064957814 0.9283482572710673 chr21 48129895 967518 0.020102225446367587 0.3591001563958146 chr22 51304566 772610 0.015059283417386281 0.2912204344773529 chrMT 16571 9507 0.5737131132701708 1.4265103997962982 chrX 155270560 3279823 0.021123276685548118 0.3825221855801341 chrY 59373566 350410 0.005901784642680886 0.2181248680912973