BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234093.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 6,218,685 number of mapped reads = 5,892,307 (94.75%) number of supplementary alignments = 43,850 (0.71%) number of secondary alignments = 0 number of mapped bases = 381,783,578 bp number of sequenced bases = 381,641,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 904,820 duplication rate = 12.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1158 >>>>>>> ACTG content number of A's = 98,477,085 bp (25.8%) number of C's = 69,434,256 bp (18.19%) number of T's = 123,391,056 bp (32.33%) number of G's = 90,300,983 bp (23.66%) number of N's = 37,637 bp (0.01%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 2,038,575 number of insertions = 25,302 mapped reads with insertion percentage = 0.43% number of deletions = 82,296 mapped reads with deletion percentage = 1.38% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.1233X std coverageData = 1.2533X There is a 8.28% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 34859279 0.13985633760968644 2.439525046882266 chr2 243199373 23415432 0.09628080743448299 2.2255243151314703 chr3 198022430 37798348 0.19087912414770386 0.6152746641453533 chr4 191154276 16036348 0.08389217513502026 0.5090079721620454 chr5 180915260 24124226 0.13334544581811397 0.527720538638273 chr6 171115067 25114162 0.14676768352608013 0.852604765056899 chr7 159138663 26668755 0.16758187166622104 1.7756760133158032 chr8 146364022 19136041 0.1307427927882441 1.4371225291881595 chr9 141213431 15222714 0.10779933531959861 0.8206948080908094 chr10 135534747 13268194 0.09789514713891044 0.813866195538693 chr11 135006516 18047741 0.13368051805736547 1.0510551524557399 chr12 133851895 14594777 0.10903676036861489 0.4895340518320208 chr13 115169878 16972033 0.14736520776726011 0.6076280737729812 chr14 107349540 17834233 0.1661323653552684 0.6355302876806793 chr15 102531392 8955602 0.0873449762585882 0.4618392613431789 chr16 90354753 9308227 0.10301867573031825 0.580994290380746 chr17 81195210 10469339 0.12894035251586886 0.6364126634580848 chr18 78077248 8198625 0.1050065827115218 1.9953458624064195 chr19 59128983 10609644 0.17943220839769897 1.3797322392208369 chr20 63025520 9665163 0.15335316551136746 0.6303342784404014 chr21 48129895 6786896 0.14101206744789282 0.5769047575960949 chr22 51304566 2800537 0.05458650600416345 0.3124093382723595 chrMT 16571 326700 19.715165047371915 12.895058115980282 chrX 155270560 10731426 0.06911436398503361 0.5409575816751455 chrY 59373566 839136 0.014133158180190827 0.3105620307886075