BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524427.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 = 3,181,017 number of mapped reads = 2,921,186 (91.83%) number of supplementary alignments = 14,204 (0.45%) number of secondary alignments = 0 number of mapped bases = 171,594,832 bp number of sequenced bases = 171,548,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 219,745 duplication rate = 5.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0071 >>>>>>> ACTG content number of A's = 43,008,379 bp (25.07%) number of C's = 34,733,994 bp (20.25%) number of T's = 52,691,542 bp (30.72%) number of G's = 41,097,040 bp (23.96%) number of N's = 17,227 bp (0.01%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 870,781 number of insertions = 13,543 mapped reads with insertion percentage = 0.46% number of deletions = 28,640 mapped reads with deletion percentage = 0.97% homopolymer indels = 39.7% >>>>>>> Coverage mean coverageData = 0.0554X std coverageData = 0.5151X There is a 4.47% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14053579 0.05638332592158316 1.0675281565722439 chr2 243199373 14445900 0.059399413007532716 0.6895459942747336 chr3 198022430 11140941 0.056261005382067075 0.2847663042989601 chr4 191154276 10964406 0.05735893661097071 0.41663307225613105 chr5 180915260 9883533 0.05463073153696377 0.2816895572288806 chr6 171115067 9473068 0.05536080583716219 0.31607163088533297 chr7 159138663 9502356 0.059711171508334215 0.6719283929806679 chr8 146364022 8663370 0.05919057075378811 0.39470086831794027 chr9 141213431 7165928 0.05074537138043193 0.3635226023247623 chr10 135534747 8389445 0.06189885018931714 0.5713635647862817 chr11 135006516 7822035 0.057938203516043625 0.4086733900100966 chr12 133851895 7682949 0.057398881054317535 0.2978553961959557 chr13 115169878 5183320 0.045005865162069544 0.25541367788003444 chr14 107349540 5118646 0.047682048754004905 0.27733385171055674 chr15 102531392 4905512 0.047844000791484424 0.2645111683601523 chr16 90354753 5347272 0.05918086013693159 0.32423227738911187 chr17 81195210 4868134 0.059955925971495114 0.32939754476315625 chr18 78077248 4538165 0.058124038900551414 0.7097990417664918 chr19 59128983 3896785 0.06590312909660563 0.6546990475341424 chr20 63025520 3954390 0.0627426794733308 0.3311548929834765 chr21 48129895 2299630 0.04777965960657093 0.3725587359558681 chr22 51304566 2157530 0.04205337201371122 0.2527675851009959 chrMT 16571 7886 0.4758916178866695 0.911279815674078 chrX 155270560 9489114 0.061113413901514875 0.3399822257999916 chrY 59373566 640938 0.010795005979597047 0.36876777938953575