BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234042.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 = 3,814,930 number of mapped reads = 3,483,809 (91.32%) number of supplementary alignments = 23,360 (0.61%) number of secondary alignments = 0 number of mapped bases = 226,031,410 bp number of sequenced bases = 225,927,783 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,772 duplication rate = 6.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3564 >>>>>>> ACTG content number of A's = 58,032,697 bp (25.69%) number of C's = 42,307,387 bp (18.73%) number of T's = 71,017,888 bp (31.43%) number of G's = 54,483,366 bp (24.12%) number of N's = 86,445 bp (0.04%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,607,856 number of insertions = 17,008 mapped reads with insertion percentage = 0.48% number of deletions = 57,561 mapped reads with deletion percentage = 1.63% homopolymer indels = 43.52% >>>>>>> Coverage mean coverageData = 0.073X std coverageData = 1.1639X There is a 5.88% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 19687287 0.07898590952758348 2.950619720673214 chr2 243199373 12815017 0.05269346233059573 1.2521233644153502 chr3 198022430 19432846 0.09813456990705548 0.3799182628140215 chr4 191154276 8284304 0.04333831381307944 0.3238792014905118 chr5 180915260 12517890 0.0691920073519503 0.3305779930431123 chr6 171115067 14050673 0.08211242438399653 0.5644207916280973 chr7 159138663 15558064 0.09776419951448254 1.9053903079195285 chr8 146364022 12872932 0.08795147758374663 0.942289411933308 chr9 141213431 8542033 0.0604902305645417 0.7699082038812629 chr10 135534747 8761381 0.06464306160544941 0.8774154415515073 chr11 135006516 9907270 0.07338364320134 0.6589679698171783 chr12 133851895 7676861 0.057353397947784004 0.3086086454444324 chr13 115169878 9683443 0.08407964971535352 0.359490126453307 chr14 107349540 11261651 0.10490637407482137 0.47255272740854903 chr15 102531392 4214678 0.0411062204246676 0.2998229616048738 chr16 90354753 6573829 0.07275576305321757 0.46455996137464634 chr17 81195210 5903077 0.07270228132915722 0.39147677292082644 chr18 78077248 5270556 0.06750437720345881 1.7885363674897345 chr19 59128983 8296871 0.14031817526778703 1.6463680032437378 chr20 63025520 7445573 0.11813584402000968 0.4884696575706368 chr21 48129895 3808916 0.07913825700222284 0.3754876074292379 chr22 51304566 2022128 0.03941419171151355 0.23277120109079164 chrMT 16571 136742 8.251885824633396 5.369780553887192 chrX 155270560 10647149 0.06857158884465929 0.449866399334693 chrY 59373566 660239 0.011120083304411933 0.22807241608735665