BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716803.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 = 757,280 number of mapped reads = 690,419 (91.17%) number of supplementary alignments = 3,193 (0.42%) number of secondary alignments = 0 number of mapped bases = 40,542,362 bp number of sequenced bases = 40,531,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,270 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.173 >>>>>>> ACTG content number of A's = 10,420,450 bp (25.71%) number of C's = 8,172,847 bp (20.16%) number of T's = 12,396,383 bp (30.58%) number of G's = 9,541,221 bp (23.54%) number of N's = 525 bp (0%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 194,829 number of insertions = 2,381 mapped reads with insertion percentage = 0.34% number of deletions = 7,074 mapped reads with deletion percentage = 1.02% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.1408X There is a 1.22% of reference with a coverageData >= 1X There is a 0.07% 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 3292956 0.013211425459196749 0.20296260631604263 chr2 243199373 3320012 0.013651400326595415 0.16871098396187814 chr3 198022430 2576778 0.01301255620386034 0.12019926260520628 chr4 191154276 2565146 0.013419244673344372 0.12766783359941417 chr5 180915260 2447447 0.01352814019115911 0.12256175017116218 chr6 171115067 2372384 0.013864261292665712 0.13307610433305675 chr7 159138663 2216081 0.01392547202687005 0.15296537903071386 chr8 146364022 2037401 0.013920094379478038 0.13822497189579022 chr9 141213431 1706996 0.01208805697809297 0.1247090863407143 chr10 135534747 2004987 0.014793158539632645 0.1480339672635281 chr11 135006516 1828489 0.013543709253263005 0.13605334141233105 chr12 133851895 1853160 0.01384485441913243 0.12493150931164025 chr13 115169878 1231076 0.010689218581962898 0.10906639263517802 chr14 107349540 1244941 0.01159707810578415 0.11531947188125201 chr15 102531392 1199236 0.011696281271593386 0.1146610413540149 chr16 90354753 1202915 0.013313245402817935 0.12434415857941322 chr17 81195210 1171366 0.014426540678939066 0.12938698302826754 chr18 78077248 1033710 0.01323958037045568 0.17356644709855307 chr19 59128983 869315 0.014702011702112312 0.16753137865254342 chr20 63025520 897749 0.014244214089784582 0.12697821412884547 chr21 48129895 555044 0.011532208827798191 0.11758413833231487 chr22 51304566 514635 0.010030978529279441 0.10564522225785625 chrMT 16571 23225 1.4015448675396778 1.4521125189495474 chrX 155270560 2253309 0.01451214576671843 0.13172863117001624 chrY 59373566 124004 0.0020885388625638554 0.06480249856913735