BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237310.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 = 3,509,122 number of mapped reads = 3,171,054 (90.37%) number of supplementary alignments = 18,142 (0.52%) number of secondary alignments = 0 number of mapped bases = 215,755,575 bp number of sequenced bases = 215,665,491 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,788 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.261 >>>>>>> ACTG content number of A's = 61,062,816 bp (28.31%) number of C's = 40,121,411 bp (18.6%) number of T's = 67,714,509 bp (31.4%) number of G's = 46,762,989 bp (21.68%) number of N's = 3,766 bp (0%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,652,069 number of insertions = 17,280 mapped reads with insertion percentage = 0.54% number of deletions = 51,567 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.0697X std coverageData = 0.6394X There is a 5.3% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 15414336 0.061842718538302054 0.9016716496071239 chr2 243199373 16975275 0.06979983044610892 0.7345426520418515 chr3 198022430 18209324 0.09195586580772694 0.37596818998206644 chr4 191154276 8778397 0.04592310035481498 0.419956826840715 chr5 180915260 12695200 0.07017207945863715 0.33822818863401743 chr6 171115067 19713990 0.11520896637348714 0.6419607363355444 chr7 159138663 14822576 0.09314251936375763 0.9032166817204389 chr8 146364022 11249746 0.0768614161204179 1.224810818720259 chr9 141213431 10527994 0.07455377243826049 0.6444768683822469 chr10 135534747 9466358 0.0698445100576312 0.6898704257401893 chr11 135006516 9463136 0.07009392050380739 0.5647350695687119 chr12 133851895 8498873 0.06349460349440701 0.3355298137023328 chr13 115169878 6556319 0.05692737644473323 0.2947511957137712 chr14 107349540 6993633 0.06514823444981692 0.35577350068088 chr15 102531392 6065611 0.059158574575872334 0.3140650182244881 chr16 90354753 5087900 0.056310264054399 0.3645419858051598 chr17 81195210 6148453 0.07572433152152695 0.4859021899177347 chr18 78077248 6074793 0.07780490675081171 1.185457839872257 chr19 59128983 3205986 0.05422021210816361 0.6330383283461689 chr20 63025520 3573769 0.05670352263654469 0.3294761476543524 chr21 48129895 3061561 0.06361038186349668 0.41943339813231323 chr22 51304566 1910719 0.037242669590071185 0.23323829699639426 chrMT 16571 83345 5.029569730251644 4.255969113498663 chrX 155270560 10615076 0.06836502682800912 0.3805936256351534 chrY 59373566 563205 0.009485786991470244 0.35171698129759044