BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524868.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 = 1,104,374 number of mapped reads = 1,015,664 (91.97%) number of supplementary alignments = 5,304 (0.48%) number of secondary alignments = 0 number of mapped bases = 59,408,100 bp number of sequenced bases = 59,390,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,316 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8689 >>>>>>> ACTG content number of A's = 14,721,655 bp (24.79%) number of C's = 11,335,421 bp (19.09%) number of T's = 19,639,293 bp (33.07%) number of G's = 13,686,654 bp (23.05%) number of N's = 7,824 bp (0.01%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 286,420 number of insertions = 4,291 mapped reads with insertion percentage = 0.42% number of deletions = 11,168 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 0.2094X There is a 1.79% of reference with a coverageData >= 1X There is a 0.09% 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 4982623 0.019990413584566356 0.38368701835758695 chr2 243199373 3776179 0.015527091839994176 0.21272398015517488 chr3 198022430 4314064 0.02178573407063028 0.15471279872463461 chr4 191154276 3252545 0.01701528769359049 0.1439555846655629 chr5 180915260 3595401 0.019873398186532193 0.14801911449632302 chr6 171115067 3848387 0.022490053432875082 0.1680255563191568 chr7 159138663 2759772 0.01734193280233855 0.2784005874879645 chr8 146364022 6399443 0.04372278728443251 0.2776354629418486 chr9 141213431 2445473 0.017317566627214093 0.1803800118593109 chr10 135534747 2982631 0.022006393681466792 0.20401621750612278 chr11 135006516 2896648 0.021455616260773667 0.18832523526637737 chr12 133851895 2392752 0.01787611598625481 0.14136166955008703 chr13 115169878 1591351 0.013817423684342186 0.12291553437566925 chr14 107349540 1250095 0.01164508948990373 0.1212250870227113 chr15 102531392 1737498 0.01694601005709549 0.13796544533586338 chr16 90354753 1724237 0.019082969547822237 0.15321384463038795 chr17 81195210 1528675 0.018827157414827794 0.1567065617332188 chr18 78077248 1455693 0.018644266252826943 0.32067813034611103 chr19 59128983 878918 0.014864419366049302 0.27815985812214344 chr20 63025520 1273124 0.020200134802537132 0.15046466746924986 chr21 48129895 843008 0.017515267797696212 0.1425239281987446 chr22 51304566 362894 0.007073327547493531 0.08738144226424147 chrMT 16571 2655 0.16021966085329792 0.4158480781105297 chrX 155270560 2969160 0.01912249173313988 0.16046319675498108 chrY 59373566 144874 0.0024400420887638785 0.06568916280383585