BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716616.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 = 541,249 number of mapped reads = 484,487 (89.51%) number of supplementary alignments = 1,407 (0.26%) number of secondary alignments = 0 number of mapped bases = 27,618,196 bp number of sequenced bases = 27,609,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,819 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7871 >>>>>>> ACTG content number of A's = 6,381,505 bp (23.11%) number of C's = 5,518,514 bp (19.99%) number of T's = 9,039,474 bp (32.74%) number of G's = 6,669,416 bp (24.16%) number of N's = 309 bp (0%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 139,076 number of insertions = 1,941 mapped reads with insertion percentage = 0.4% number of deletions = 5,564 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0089X std coverageData = 0.112X There is a 0.85% of reference with a coverageData >= 1X There is a 0.03% 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 2199733 0.008825386236449939 0.13618614748520008 chr2 243199373 2357675 0.0096944123289331 0.14527604151821596 chr3 198022430 1807214 0.009126309580182406 0.10009648064253741 chr4 191154276 1769778 0.009258375156619567 0.10392237104770954 chr5 180915260 1650082 0.0091207452594104 0.0986544838132549 chr6 171115067 1608140 0.009398003508364346 0.10784465912971934 chr7 159138663 1548656 0.009731488067107866 0.13662376382452657 chr8 146364022 1370990 0.009366987742383849 0.1068269779677095 chr9 141213431 1138140 0.00805971494312039 0.09861255631295499 chr10 135534747 1358258 0.010021474419397412 0.12188893443580757 chr11 135006516 1241230 0.00919385253968038 0.10729452807270361 chr12 133851895 1243632 0.009291104918611725 0.10013843373806311 chr13 115169878 860376 0.0074704950195397446 0.08977136091589259 chr14 107349540 830589 0.007737238557333361 0.09198828774375924 chr15 102531392 793947 0.007743452853931799 0.09124312686158932 chr16 90354753 848290 0.009388438038229157 0.1047235765446688 chr17 81195210 783318 0.009647342497174402 0.10430006865489665 chr18 78077248 706643 0.009050562335393789 0.14090953119091937 chr19 59128983 601186 0.010167365807729182 0.12363823035959208 chr20 63025520 589816 0.0093583678484525 0.1007239554566081 chr21 48129895 367361 0.007632698970151504 0.09261343295033556 chr22 51304566 336112 0.0065513077335066046 0.08389596153677782 chrMT 16571 8775 0.5295395570575101 0.7680147706554031 chrX 155270560 1516710 0.00976817498436278 0.10579422179196003 chrY 59373566 81545 0.0013734226440096254 0.04789733672764124