BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238627.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 = 4,774,684 number of mapped reads = 4,210,385 (88.18%) number of supplementary alignments = 43,413 (0.91%) number of secondary alignments = 0 number of mapped bases = 256,275,267 bp number of sequenced bases = 256,162,223 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,061,319 duplication rate = 22.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2835 >>>>>>> ACTG content number of A's = 64,116,036 bp (25.03%) number of C's = 44,206,603 bp (17.26%) number of T's = 87,131,319 bp (34.01%) number of G's = 60,702,530 bp (23.7%) number of N's = 5,735 bp (0%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,427,086 number of insertions = 16,356 mapped reads with insertion percentage = 0.38% number of deletions = 66,861 mapped reads with deletion percentage = 1.57% homopolymer indels = 42.01% >>>>>>> Coverage mean coverageData = 0.0828X std coverageData = 1.422X There is a 1.62% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 6715699 0.026943559751451934 1.0822904318954982 chr2 243199373 10962880 0.0450777477950159 2.6135402692733174 chr3 198022430 12023454 0.06071763688588207 0.9131482012076572 chr4 191154276 11305355 0.05914256921984837 0.8926603893282821 chr5 180915260 30653986 0.1694383657851748 1.5576388085545756 chr6 171115067 26632884 0.1556431263881631 1.7630578464311346 chr7 159138663 3808860 0.023934221440581036 0.6777985792816824 chr8 146364022 21771379 0.14874816025484733 1.6289562161266746 chr9 141213431 4404300 0.031188959639398606 0.7033943482317424 chr10 135534747 16910004 0.12476508330369333 1.3061630164833549 chr11 135006516 16538640 0.1225025316555832 1.3522462529636705 chr12 133851895 12007221 0.08970527462461401 1.1238159217388082 chr13 115169878 5552272 0.048209411144813405 1.0537912338836128 chr14 107349540 6901691 0.06429176128747267 1.033052397645568 chr15 102531392 2525438 0.024630875976013277 0.7942309130611844 chr16 90354753 3009063 0.03330276382914798 0.7067477181879565 chr17 81195210 3269685 0.04026943214999998 0.7213649403811827 chr18 78077248 10180857 0.13039467016050565 2.9134895105232053 chr19 59128983 2410929 0.040774065063828344 1.022333386673215 chr20 63025520 1901245 0.0301662723290502 0.6508962164193516 chr21 48129895 7374999 0.15323114667089965 1.4667780500379055 chr22 51304566 3457064 0.06738316429769624 0.9482637673746894 chrMT 16571 11455 0.6912678776175246 3.077997801340146 chrX 155270560 34999249 0.22540814562657596 1.8239652398978774 chrY 59373566 946658 0.01594409875937046 0.5293980540439274