BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238282.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 = 2,120,761 number of mapped reads = 1,808,903 (85.29%) number of supplementary alignments = 23,249 (1.1%) number of secondary alignments = 0 number of mapped bases = 118,854,350 bp number of sequenced bases = 118,792,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,671 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1725 >>>>>>> ACTG content number of A's = 33,078,532 bp (27.85%) number of C's = 22,991,468 bp (19.35%) number of T's = 36,308,844 bp (30.56%) number of G's = 26,387,582 bp (22.21%) number of N's = 26,353 bp (0.02%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,031,660 number of insertions = 9,162 mapped reads with insertion percentage = 0.5% number of deletions = 37,034 mapped reads with deletion percentage = 2.02% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0384X std coverageData = 0.3374X There is a 3.15% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 4672389 0.018745746675592034 0.36810791985887387 chr2 243199373 8423284 0.03463530310993031 0.45486027496947823 chr3 198022430 5236533 0.026444140696586745 0.1892725939479456 chr4 191154276 7346230 0.03843089547209501 0.23780115673163738 chr5 180915260 7140576 0.039469174684324586 0.23746914713289202 chr6 171115067 4724886 0.027612331765033877 0.24416871726915051 chr7 159138663 5403780 0.03395642453022243 0.46579772159078137 chr8 146364022 12239723 0.08362521631169714 0.5603281314300901 chr9 141213431 3641362 0.025786229923129622 0.3333188175789202 chr10 135534747 7368570 0.05436664887123005 0.34602936872498946 chr11 135006516 5790212 0.04288838917967485 0.30088537893887346 chr12 133851895 6186132 0.04621624520145942 0.2560769677658112 chr13 115169878 2071127 0.017983235165014242 0.1561385637475196 chr14 107349540 5028937 0.046846376798633696 0.27309355311715255 chr15 102531392 4264200 0.041589213964831374 0.2396991755609832 chr16 90354753 4042845 0.044744132054680065 0.2728672027149198 chr17 81195210 4872577 0.0600106459482031 0.35975436240833236 chr18 78077248 7370884 0.09440501796374791 0.6614408545086992 chr19 59128983 1390919 0.023523472406078758 0.3579386749897236 chr20 63025520 5820530 0.09235195520798559 0.36383218739443873 chr21 48129895 816700 0.016968663654886428 0.17505006620453903 chr22 51304566 3207175 0.06251246721393179 0.29645221802361477 chrMT 16571 11364 0.6857763562850764 0.962984110157748 chrX 155270560 1531974 0.009866480806148957 0.16717885360685872 chrY 59373566 251441 0.00423489806894873 0.126019989954649