BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231771.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 = 1,760,883 number of mapped reads = 1,100,590 (62.5%) number of supplementary alignments = 10,662 (0.61%) number of secondary alignments = 0 number of mapped bases = 69,975,015 bp number of sequenced bases = 69,936,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,025 duplication rate = 8.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.648 >>>>>>> ACTG content number of A's = 18,442,426 bp (26.37%) number of C's = 13,322,113 bp (19.05%) number of T's = 21,780,753 bp (31.14%) number of G's = 16,373,928 bp (23.41%) number of N's = 16,845 bp (0.02%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 628,802 number of insertions = 5,803 mapped reads with insertion percentage = 0.52% number of deletions = 23,592 mapped reads with deletion percentage = 2.11% homopolymer indels = 45.24% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2687X There is a 1.39% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 5497200 0.022054909945440015 0.3792827210240779 chr2 243199373 5985640 0.02461207003194042 0.3623070012120312 chr3 198022430 5304879 0.026789283416025145 0.2479337486446025 chr4 191154276 4048228 0.021177805093933657 0.22531408396562153 chr5 180915260 4007335 0.022150342652134485 0.223882790680161 chr6 171115067 4216773 0.024642908856179216 0.267984421886768 chr7 159138663 3686705 0.023166620420833874 0.27075275422632983 chr8 146364022 3832039 0.02618156393652533 0.2767108644185876 chr9 141213431 2769116 0.019609437858641082 0.23495367923687352 chr10 135534747 3221336 0.02376760256172537 0.26017660550688254 chr11 135006516 3075384 0.02277952273059176 0.2458181686493443 chr12 133851895 3356374 0.025075281900192748 0.24221288824725354 chr13 115169878 2500332 0.021709947456920984 0.22912672748057797 chr14 107349540 1960918 0.01826666420741067 0.20972561192033265 chr15 102531392 1806830 0.017622212717057426 0.20311803052780972 chr16 90354753 1948867 0.021569059017847128 0.22649608266991583 chr17 81195210 2006012 0.024706038693661857 0.24834202359635557 chr18 78077248 2011397 0.025761627766388486 0.34009539523015453 chr19 59128983 1449610 0.02451606515877332 0.29825551784371634 chr20 63025520 1705377 0.02705851534426055 0.25669945890062357 chr21 48129895 1092350 0.022695873323638042 0.23672294958696186 chr22 51304566 790596 0.015409856502830567 0.1859512414417387 chrMT 16571 46082 2.780882264196488 3.466010206989742 chrX 155270560 3444145 0.022181571316545776 0.22803748592491596 chrY 59373566 211490 0.0035620228705818342 0.10217197099442632