BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237790.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 = 779,233 number of mapped reads = 510,764 (65.55%) number of supplementary alignments = 3,799 (0.49%) number of secondary alignments = 0 number of mapped bases = 31,524,304 bp number of sequenced bases = 31,510,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,621 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7698 >>>>>>> ACTG content number of A's = 8,888,064 bp (28.21%) number of C's = 5,570,177 bp (17.68%) number of T's = 9,837,718 bp (31.22%) number of G's = 7,187,552 bp (22.81%) number of N's = 27,447 bp (0.09%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 269,146 number of insertions = 2,199 mapped reads with insertion percentage = 0.43% number of deletions = 8,544 mapped reads with deletion percentage = 1.65% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.0102X std coverageData = 0.1327X There is a 0.91% of reference with a coverageData >= 1X There is a 0.08% 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 3710072 0.014884905743123504 0.1832494316468939 chr2 243199373 2612832 0.010743580329871985 0.1287142287979086 chr3 198022430 2303660 0.011633328608279375 0.1192663157867061 chr4 191154276 1747869 0.009143760927430156 0.10674035283091121 chr5 180915260 1261606 0.006973463708920961 0.09166390124368752 chr6 171115067 2341431 0.013683371318786323 0.1300810511186139 chr7 159138663 1363073 0.008565316399572868 0.11631023448230227 chr8 146364022 1469149 0.010037637528162488 0.15186283579533136 chr9 141213431 927286 0.006566556689639529 0.09872873060522581 chr10 135534747 1213104 0.00895050182223751 0.15350796737871428 chr11 135006516 1639207 0.012141688035264905 0.14404860411629533 chr12 133851895 886154 0.006620406830997798 0.08906830136118246 chr13 115169878 998100 0.008666328534271782 0.10469478409020053 chr14 107349540 818260 0.0076223894392095206 0.09855726875085313 chr15 102531392 555170 0.0054146343785130705 0.08067140779790713 chr16 90354753 1365993 0.015118108949951975 0.21771608571661621 chr17 81195210 1251488 0.01541332302730666 0.17682614647541334 chr18 78077248 633968 0.008119753401144467 0.18284607371590916 chr19 59128983 495875 0.00838632722636207 0.13711248695460015 chr20 63025520 532181 0.008443897011877094 0.10381080908489274 chr21 48129895 656399 0.013638072553451445 0.13026192029703956 chr22 51304566 480837 0.00937220675446314 0.11081056064024339 chrMT 16571 12864 0.7762959386880696 1.2714301949706162 chrX 155270560 2146735 0.013825769675848403 0.13709344337036042 chrY 59373566 100991 0.0017009421330697906 0.04942975809387757