BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237812.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 = 3,800,043 number of mapped reads = 2,270,694 (59.75%) number of supplementary alignments = 13,899 (0.37%) number of secondary alignments = 0 number of mapped bases = 135,498,776 bp number of sequenced bases = 135,442,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 338,384 duplication rate = 11.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5252 >>>>>>> ACTG content number of A's = 36,983,828 bp (27.31%) number of C's = 26,912,982 bp (19.87%) number of T's = 41,112,241 bp (30.35%) number of G's = 30,315,220 bp (22.38%) number of N's = 117,832 bp (0.09%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,224,842 number of insertions = 10,400 mapped reads with insertion percentage = 0.45% number of deletions = 34,803 mapped reads with deletion percentage = 1.51% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.4663X There is a 2.17% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 10701940 0.04293646273402865 0.7053636816815959 chr2 243199373 14431652 0.059340827330175726 0.5639458222710092 chr3 198022430 7805061 0.03941503495336362 0.3633482443645685 chr4 191154276 9195063 0.04810283710315745 0.4221254042727708 chr5 180915260 7538573 0.04166908308342812 0.3649503384885358 chr6 171115067 6335890 0.03702707254878964 0.36999850274987267 chr7 159138663 7680282 0.048261571733828126 0.5612441583934156 chr8 146364022 7319101 0.050006148368893555 0.47053169637469294 chr9 141213431 4628365 0.03277567131698684 0.3717758394355434 chr10 135534747 7639455 0.056365287640961916 0.6148322050286439 chr11 135006516 5416731 0.040121996778288836 0.40407075610341814 chr12 133851895 7365833 0.055029725204861685 0.43055813889582834 chr13 115169878 3856198 0.0334826958833802 0.339778366170901 chr14 107349540 3367260 0.031367251317518455 0.3263645756774272 chr15 102531392 3830817 0.03736238165965795 0.34756318904422345 chr16 90354753 4631300 0.05125684976417345 0.4481540781949288 chr17 81195210 3238769 0.0398886707725739 0.3900104447494824 chr18 78077248 3911146 0.05009328709946334 0.6179186267926183 chr19 59128983 2969873 0.05022702656665006 0.5478952567811459 chr20 63025520 2954473 0.04687740775482693 0.40217232151104537 chr21 48129895 2453228 0.05097098175676469 0.4287687150792272 chr22 51304566 1616718 0.03151216599317885 0.32132943615970433 chrMT 16571 61186 3.6923541126063606 4.324782780494926 chrX 155270560 6086356 0.03919839021640677 0.36794524527308087 chrY 59373566 463506 0.007806605383951505 0.20652584269062452