BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524665.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 = 1,839,890 number of mapped reads = 1,705,479 (92.69%) number of supplementary alignments = 7,574 (0.41%) number of secondary alignments = 0 number of mapped bases = 101,036,552 bp number of sequenced bases = 101,006,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,954 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8127 >>>>>>> ACTG content number of A's = 24,673,076 bp (24.43%) number of C's = 19,871,367 bp (19.67%) number of T's = 31,273,085 bp (30.96%) number of G's = 25,176,267 bp (24.93%) number of N's = 12,849 bp (0.01%) GC percentage = 44.6% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 498,758 number of insertions = 6,039 mapped reads with insertion percentage = 0.35% number of deletions = 18,633 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.3032X There is a 2.91% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8035605 0.03223905708945054 0.5393708288464244 chr2 243199373 8524509 0.03505152540010866 0.4038998274102422 chr3 198022430 6694329 0.03380591279482834 0.20145613323448247 chr4 191154276 6451154 0.0337484158607051 0.2276348647045999 chr5 180915260 6096358 0.03369731221125294 0.2016673904380664 chr6 171115067 5893813 0.03444356539333851 0.22867382096789857 chr7 159138663 5552668 0.034892011126171144 0.3527836896631912 chr8 146364022 5077776 0.03469278809515087 0.3398518631495457 chr9 141213431 4341060 0.030741126883320327 0.25305611393382677 chr10 135534747 4836468 0.03568434004602525 0.31015825442640865 chr11 135006516 4611473 0.03415741059490788 0.26508778383666615 chr12 133851895 4520989 0.033776055243745336 0.20426473405813908 chr13 115169878 3141065 0.027273320546540823 0.18268296166190126 chr14 107349540 3053990 0.028449027354937897 0.19288771314907335 chr15 102531392 2990625 0.029167896208802082 0.1880057675275352 chr16 90354753 2924479 0.032366631559493056 0.211550606796338 chr17 81195210 2839116 0.034966545440303684 0.21897526876677173 chr18 78077248 2658681 0.034051930211474665 0.47514168375964827 chr19 59128983 2165438 0.03662227709886368 0.4241761987814403 chr20 63025520 2146413 0.03405625213405617 0.20605688278771916 chr21 48129895 1324473 0.02751871783638838 0.21081938729316815 chr22 51304566 1205795 0.023502683952145702 0.16788680473521123 chrMT 16571 17379 1.048759881721079 1.2176363029988886 chrX 155270560 5608031 0.036117799794114225 0.22888639322699386 chrY 59373566 324865 0.005471542672710613 0.18805583376196647