BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714064.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 426,634 number of mapped reads = 183,171 (42.93%) number of supplementary alignments = 6,913 (1.62%) number of secondary alignments = 0 number of mapped bases = 22,549,229 bp number of sequenced bases = 22,193,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,271 duplication rate = 36.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.0302 >>>>>>> ACTG content number of A's = 5,656,655 bp (25.49%) number of C's = 4,158,750 bp (18.74%) number of T's = 5,494,225 bp (24.76%) number of G's = 6,883,458 bp (31.02%) number of N's = 385 bp (0%) GC percentage = 49.75% >>>>>>> Mismatches and indels general error rate = 0.0386 number of mismatches = 769,236 number of insertions = 25,398 mapped reads with insertion percentage = 13.22% number of deletions = 63,532 mapped reads with deletion percentage = 33.32% homopolymer indels = 27.31% >>>>>>> Coverage mean coverageData = 0.0073X std coverageData = 6.9781X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 565381 0.0022683233354913084 0.9299058222272419 chr2 243199373 4018766 0.016524573852416964 12.57130158278918 chr3 198022430 1201145 0.0060657017490392375 4.372756943860638 chr4 191154276 711403 0.0037216169833417696 1.4225178859753276 chr5 180915260 1062111 0.00587076513059208 3.8538148191906747 chr6 171115067 301735 0.001763345597147211 0.789454499209853 chr7 159138663 606807 0.003813070868893752 2.5255070657491436 chr8 146364022 4312614 0.02946498696243808 23.185505894706097 chr9 141213431 200462 0.0014195675197495909 0.3862034317889565 chr10 135534747 865685 0.0063871812886477 2.4266598044493977 chr11 135006516 476656 0.0035306147741787515 2.510118582766449 chr12 133851895 350910 0.00262162892800285 0.6654786093870312 chr13 115169878 652671 0.005667028665255684 2.9999767238025 chr14 107349540 1320395 0.012299959552691144 7.244706698703604 chr15 102531392 839185 0.008184664068542052 4.014389836519394 chr16 90354753 1293720 0.014318228505367061 7.054330838445541 chr17 81195210 100273 0.001234962013153239 0.3199324102302792 chr18 78077248 438502 0.005616258400910852 3.063786495256653 chr19 59128983 53192 8.995926752198664E-4 0.2345061424037927 chr20 63025520 203941 0.0032358479549236562 0.7379802534881037 chr21 48129895 1241062 0.025785678526828285 13.743052421657017 chr22 51304566 29374 5.725416330390554E-4 0.13466946139946906 chrMT 16571 298211 17.995956791986 145.0018356692186 chrX 155270560 1394877 0.008983525273561195 2.055642315897643 chrY 59373566 10151 1.7096833968166912E-4 0.06020896429336934