BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237797.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 = 1,621,816 number of mapped reads = 1,079,354 (66.55%) number of supplementary alignments = 12,079 (0.74%) number of secondary alignments = 0 number of mapped bases = 70,207,239 bp number of sequenced bases = 70,178,187 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 263,532 duplication rate = 14.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5936 >>>>>>> ACTG content number of A's = 19,183,066 bp (27.33%) number of C's = 12,899,807 bp (18.38%) number of T's = 22,238,788 bp (31.69%) number of G's = 15,740,012 bp (22.43%) number of N's = 116,514 bp (0.17%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 602,068 number of insertions = 4,914 mapped reads with insertion percentage = 0.45% number of deletions = 16,744 mapped reads with deletion percentage = 1.53% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 0.4255X There is a 0.72% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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% 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 5566412 0.02233259029673591 0.5234622330752845 chr2 243199373 6120410 0.02516622442114602 0.4698386987724394 chr3 198022430 4565868 0.023057327394679483 0.38171361709380824 chr4 191154276 4879381 0.025525879421080803 0.4011630339971299 chr5 180915260 3916468 0.02164807988004992 0.3784591772854199 chr6 171115067 4052414 0.02368239145182931 0.4135541595233005 chr7 159138663 3715102 0.023345062286969195 0.42063186068942643 chr8 146364022 3687796 0.025196055353001984 0.6578093923205687 chr9 141213431 2549015 0.018050797165320626 0.3436833090760338 chr10 135534747 3302388 0.024365618950836276 0.4335542120785651 chr11 135006516 3693243 0.02735603517092464 0.4362686562851231 chr12 133851895 3894979 0.02909916964567442 0.44018058359872536 chr13 115169878 2343531 0.0203484716724281 0.36813759312466765 chr14 107349540 2070740 0.019289696071357176 0.3428578156699825 chr15 102531392 1706612 0.016644775484955868 0.3149345900025184 chr16 90354753 1735919 0.019212259923946668 0.3480759992726907 chr17 81195210 1762377 0.02170543065286733 0.3877811460618703 chr18 78077248 2032537 0.026032385260300158 0.4838438116618608 chr19 59128983 1510029 0.025537882158399375 0.4796455308313324 chr20 63025520 1440929 0.022862627710172008 0.38714369869049947 chr21 48129895 849745 0.01765524317059075 0.3325729792739813 chr22 51304566 758153 0.014777495632649929 0.30105889470526953 chrMT 16571 45563 2.749562488685052 4.1635857389870425 chrX 155270560 3793971 0.024434580515456376 0.394703406139487 chrY 59373566 213657 0.00359852059416475 0.11762213893521016