BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524529.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 = 744,844 number of mapped reads = 686,266 (92.14%) number of supplementary alignments = 2,984 (0.4%) number of secondary alignments = 0 number of mapped bases = 40,571,248 bp number of sequenced bases = 40,558,657 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,716 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2311 >>>>>>> ACTG content number of A's = 9,897,172 bp (24.4%) number of C's = 7,436,857 bp (18.34%) number of T's = 13,097,178 bp (32.29%) number of G's = 10,127,003 bp (24.97%) number of N's = 447 bp (0%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 207,301 number of insertions = 2,937 mapped reads with insertion percentage = 0.43% number of deletions = 7,396 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.82% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.1559X There is a 1.2% 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 4107744 0.0164803761913195 0.27095056652989535 chr2 243199373 3250650 0.013366193999192588 0.1745541502968101 chr3 198022430 2262787 0.011426922697595418 0.11454348215767726 chr4 191154276 2099349 0.010982485162926724 0.12459320266195933 chr5 180915260 2206609 0.012196920259794557 0.1184938223143436 chr6 171115067 1804481 0.010545424383932247 0.12307984384410012 chr7 159138663 2130541 0.013387953372462354 0.18041573726529603 chr8 146364022 3794668 0.025926234795597514 0.19445571485024085 chr9 141213431 1416831 0.01003325951339572 0.1203053799532762 chr10 135534747 2148669 0.01585327045322186 0.16605607132133718 chr11 135006516 1454162 0.010771050487666833 0.13706709014786722 chr12 133851895 1922037 0.014359430622928424 0.12832995569893793 chr13 115169878 920596 0.007993374795447816 0.09535583447029033 chr14 107349540 997455 0.009291656023863726 0.1028252063002255 chr15 102531392 1105749 0.010784492226536825 0.1111525357377543 chr16 90354753 1321279 0.01462323736306379 0.1332004424875377 chr17 81195210 1515095 0.018659906169341763 0.15146582082588245 chr18 78077248 989072 0.012667864523093847 0.19578602717040508 chr19 59128983 838196 0.014175721574646397 0.1877423897362151 chr20 63025520 1339260 0.021249487509186756 0.15759157662809264 chr21 48129895 514421 0.010688180391833392 0.11914936815355284 chr22 51304566 337990 0.006587912662588355 0.08605540648459807 chrMT 16571 3561 0.2148934886247058 0.500905238536519 chrX 155270560 1942419 0.012509898850110415 0.1223860393043265 chrY 59373566 147627 0.0024864095244001346 0.10090112932211448