BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716773.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 = 2,063,796 number of mapped reads = 1,929,772 (93.51%) number of supplementary alignments = 46,446 (2.25%) number of secondary alignments = 0 number of mapped bases = 147,433,890 bp number of sequenced bases = 147,375,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,339 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0007 >>>>>>> ACTG content number of A's = 35,972,645 bp (24.41%) number of C's = 29,673,857 bp (20.13%) number of T's = 44,573,008 bp (30.24%) number of G's = 37,149,953 bp (25.21%) number of N's = 5,559 bp (0%) GC percentage = 45.34% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 965,890 number of insertions = 12,671 mapped reads with insertion percentage = 0.65% number of deletions = 28,816 mapped reads with deletion percentage = 1.47% homopolymer indels = 39.33% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.3924X There is a 3.92% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15986648 0.06413884922677886 0.7421223791325903 chr2 243199373 13887080 0.057101627478291235 0.4208937733031589 chr3 198022430 9491454 0.04793120658099186 0.2585176178393509 chr4 191154276 7082092 0.037049090128645615 0.33758448160627835 chr5 180915260 7579242 0.041893878935364545 0.24194674810465897 chr6 171115067 8234812 0.048124412095166345 0.27945862259258736 chr7 159138663 9283646 0.05833683546782092 0.5384523181239282 chr8 146364022 9135625 0.062417149208977056 0.41479764588184737 chr9 141213431 4448265 0.031500296880400847 0.27139942884825596 chr10 135534747 7927292 0.05848900134811924 0.5473325687166765 chr11 135006516 6313591 0.046765083546041586 0.33147756079943863 chr12 133851895 5721127 0.042742218927867996 0.24275058143986997 chr13 115169878 2756224 0.023931813143016442 0.176925608620832 chr14 107349540 2879504 0.02682362681759046 0.2071116964621201 chr15 102531392 3030486 0.029556664948038547 0.198205120547204 chr16 90354753 4502931 0.04983612760249591 0.28318030018464857 chr17 81195210 3719361 0.04580764062313528 0.28169555500764865 chr18 78077248 3978772 0.05095942930775429 0.41645232678259503 chr19 59128983 3697932 0.0625400913795524 0.5390230123911428 chr20 63025520 3370799 0.05348308113919568 0.2885785402616367 chr21 48129895 2276376 0.0472965087499152 0.32238547342935936 chr22 51304566 2283603 0.04451071664849479 0.2558233270925589 chrMT 16571 137125 8.274998491340293 5.918668750482969 chrX 155270560 9208741 0.059307707784399054 0.30490231748024244 chrY 59373566 501162 0.008440827017194823 0.3001142756701458