BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716639.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 504,757 number of mapped reads = 463,298 (91.79%) number of supplementary alignments = 1,550 (0.31%) number of secondary alignments = 0 number of mapped bases = 26,794,161 bp number of sequenced bases = 26,785,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,383 duplication rate = 1.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8316 >>>>>>> ACTG content number of A's = 6,806,182 bp (25.41%) number of C's = 4,961,414 bp (18.52%) number of T's = 8,209,217 bp (30.65%) number of G's = 6,808,388 bp (25.42%) number of N's = 523 bp (0%) GC percentage = 43.94% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 136,612 number of insertions = 1,762 mapped reads with insertion percentage = 0.38% number of deletions = 5,216 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.79% >>>>>>> Coverage mean coverageData = 0.0087X std coverageData = 0.1147X There is a 0.83% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 2255287 0.009048270335101792 0.1611517921749 chr2 243199373 2109265 0.008672986998202499 0.14248947705697038 chr3 198022430 1529080 0.007721751520774692 0.0912060029944916 chr4 191154276 1681479 0.008796449837198515 0.10222547060173647 chr5 180915260 1527566 0.008443544231702732 0.09429739352965104 chr6 171115067 1441304 0.00842301046464833 0.10168329812988064 chr7 159138663 1534581 0.009643043186808727 0.1347310823112948 chr8 146364022 1411756 0.009645512474370238 0.12805846265559798 chr9 141213431 891541 0.006313429209152209 0.09051678996439719 chr10 135534747 1193201 0.008803653870398267 0.1222856479270143 chr11 135006516 947570 0.007018698267867308 0.09888853819260363 chr12 133851895 1310833 0.009793159820411956 0.10180521231450505 chr13 115169878 808232 0.0070177377456282445 0.08729353350804828 chr14 107349540 913507 0.008509649878332035 0.09589799321998685 chr15 102531392 965084 0.009412570932422336 0.09978765707758985 chr16 90354753 914998 0.010126727920998245 0.10729359384840492 chr17 81195210 1158856 0.014272467550733596 0.12477664934525048 chr18 78077248 500869 0.006415044239264171 0.1231424250799369 chr19 59128983 689976 0.011668998264353709 0.1397831805816824 chr20 63025520 863447 0.013699958366071395 0.12172638561737412 chr21 48129895 343065 0.0071278983675322795 0.09461870489354353 chr22 51304566 243798 0.00475197470728044 0.0711823105924446 chrMT 16571 4465 0.2694466236195764 0.5436651835892362 chrX 155270560 1457522 0.009386982310104375 0.10275685451099276 chrY 59373566 96879 0.0016316857235760438 0.07041904454887911