BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716250.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 = 1,666,519 number of mapped reads = 1,504,425 (90.27%) number of supplementary alignments = 6,950 (0.42%) number of secondary alignments = 0 number of mapped bases = 85,283,319 bp number of sequenced bases = 85,261,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,213 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2243 >>>>>>> ACTG content number of A's = 21,499,320 bp (25.22%) number of C's = 17,295,553 bp (20.29%) number of T's = 25,943,065 bp (30.43%) number of G's = 20,521,884 bp (24.07%) number of N's = 2,004 bp (0%) GC percentage = 44.35% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 419,774 number of insertions = 4,498 mapped reads with insertion percentage = 0.3% number of deletions = 12,504 mapped reads with deletion percentage = 0.83% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2187X There is a 2.49% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6604396 0.026497009209056295 0.3038581854202664 chr2 243199373 7263338 0.029865776010861673 0.258437533247725 chr3 198022430 5385690 0.02719737355005693 0.17808714461273248 chr4 191154276 5664469 0.02963297038670482 0.19881121202082866 chr5 180915260 5193336 0.028705903526324978 0.18504225255251056 chr6 171115067 5262419 0.030753685763977755 0.20206263621582152 chr7 159138663 4330720 0.027213499965121613 0.22156856592447421 chr8 146364022 4180800 0.028564396788713555 0.21170201518045115 chr9 141213431 3403182 0.024099563164073252 0.21176059529000912 chr10 135534747 3921546 0.028933879221392577 0.21723291340477294 chr11 135006516 3899446 0.028883391080175715 0.22437170253606376 chr12 133851895 4141381 0.030940025167368754 0.19210879180939588 chr13 115169878 2634427 0.022874270996449262 0.16272841525854242 chr14 107349540 2521986 0.02349321664536243 0.17208971562753922 chr15 102531392 2624413 0.02559619009171357 0.17335408065391716 chr16 90354753 2509957 0.027778914962005373 0.19384453244931174 chr17 81195210 2325111 0.028636061166662417 0.19165987176180943 chr18 78077248 2274828 0.029135606828765277 0.3657785823646332 chr19 59128983 1726890 0.029205474411761825 0.2529003222242979 chr20 63025520 2091921 0.03319164998559314 0.2017190712406852 chr21 48129895 1131785 0.023515218555951557 0.1771640339761984 chr22 51304566 1040522 0.020281274769968816 0.15415370033021175 chrMT 16571 5107 0.30818900488805745 0.6100499396392253 chrX 155270560 4897204 0.03153981025121568 0.21487123230259692 chrY 59373566 248445 0.004184437902887625 0.09624405834555456