BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173864.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,386,552 number of mapped reads = 2,315,506 (97.02%) number of supplementary alignments = 244,509 (10.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,160,183 number of mapped paired reads (second in pair) = 1,155,323 number of mapped paired reads (both in pair) = 2,270,156 number of mapped paired reads (singletons) = 45,350 number of mapped bases = 271,930,190 bp number of sequenced bases = 271,761,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,792,206 duplication rate = 63.57% >>>>>>> Insert size mean insert size = 1,203,084.8855 std insert size = 9,950,387.165 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.7501 >>>>>>> ACTG content number of A's = 81,965,231 bp (30.16%) number of C's = 53,040,007 bp (19.52%) number of T's = 81,713,758 bp (30.07%) number of G's = 55,039,853 bp (20.25%) number of N's = 2,938 bp (0%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 2,995,484 number of insertions = 32,114 mapped reads with insertion percentage = 1.33% number of deletions = 65,827 mapped reads with deletion percentage = 2.77% homopolymer indels = 42.72% >>>>>>> Coverage mean coverageData = 0.0878X std coverageData = 1.4514X There is a 1.89% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 1.13% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 21717451 0.08713098050816892 1.0496747189553028 chr2 243199373 26318843 0.10821920581185052 3.945682575294819 chr3 198022430 20175763 0.1018862509666203 0.9198619825369859 chr4 191154276 17807216 0.09315625249209701 1.080564908174455 chr5 180915260 17043972 0.094209697954722 0.8816993567122249 chr6 171115067 15615503 0.09125732335423158 0.9262194170959188 chr7 159138663 15435755 0.09699563078521026 1.0920092460027033 chr8 146364022 15344838 0.1048402318433146 1.2284860617523772 chr9 141213431 11581417 0.08201356569262877 1.0131731697383743 chr10 135534747 12874668 0.09499164077828691 1.2675143080156552 chr11 135006516 12072830 0.0894240541693558 0.8731858448330462 chr12 133851895 11899297 0.08889898047390364 0.8568262825189706 chr13 115169878 8249274 0.07162700997217346 0.7711317008367711 chr14 107349540 8076433 0.07523491018219547 0.7850956575251725 chr15 102531392 7854917 0.07660987378382612 0.781940753147227 chr16 90354753 8257533 0.0913901341747899 1.0184755087912862 chr17 81195210 6992313 0.08611730913683209 0.8639765750991338 chr18 78077248 7496295 0.09601126054033052 1.4561724138718946 chr19 59128983 5023878 0.08496472871857107 0.9426679161735997 chr20 63025520 5588013 0.08866270361593209 0.8793747907936982 chr21 48129895 3874717 0.08050541144957828 1.0864580715459908 chr22 51304566 3088069 0.06019091945929335 0.7403577866429164 chrMT 16571 356427 21.509082131434432 17.25684580803209 chrX 155270560 6758128 0.04352485107286275 0.5920319197549758 chrY 59373566 2426640 0.040870713408050985 0.7865928069081781