BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524383.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 = 1,046,998 number of mapped reads = 963,911 (92.06%) number of supplementary alignments = 3,729 (0.36%) number of secondary alignments = 0 number of mapped bases = 56,722,076 bp number of sequenced bases = 56,705,770 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,203 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.088 >>>>>>> ACTG content number of A's = 14,691,964 bp (25.91%) number of C's = 10,148,327 bp (17.9%) number of T's = 17,620,430 bp (31.07%) number of G's = 14,237,704 bp (25.11%) number of N's = 7,345 bp (0.01%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 276,819 number of insertions = 3,810 mapped reads with insertion percentage = 0.39% number of deletions = 10,362 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 0.0183X std coverageData = 0.2036X There is a 1.71% 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 4578401 0.018368664365333718 0.39848203715672514 chr2 243199373 4823740 0.019834508372684002 0.21915924502009362 chr3 198022430 3768247 0.019029394801386892 0.14467212928108192 chr4 191154276 3682935 0.01926681985392783 0.15763161662066377 chr5 180915260 3412857 0.018864395408104324 0.14448070787453546 chr6 171115067 3221708 0.01882772836129036 0.15569817637503255 chr7 159138663 3128143 0.01965671283791042 0.26142370829022166 chr8 146364022 2866151 0.019582346541419857 0.17723386840233885 chr9 141213431 2388563 0.016914559635619927 0.17605285415901933 chr10 135534747 2724891 0.02010474111114842 0.18548308034468589 chr11 135006516 2575239 0.019074923761457557 0.18345493676899505 chr12 133851895 2533862 0.018930340881613966 0.14759704487890993 chr13 115169878 1804681 0.015669730934333367 0.13091469016577495 chr14 107349540 1711036 0.015938922514246452 0.13767541015927195 chr15 102531392 1681568 0.016400518584591146 0.13423517627884093 chr16 90354753 1651423 0.01827710159309494 0.1458859359859335 chr17 81195210 1514538 0.018653046158757396 0.15520617187704097 chr18 78077248 1526140 0.019546539345239217 0.294688351439906 chr19 59128983 1162544 0.019661153312919316 0.26359344085143177 chr20 63025520 1198889 0.019022278594448726 0.14597718865422574 chr21 48129895 752653 0.015637952253999308 0.14145859446011197 chr22 51304566 690577 0.013460341911868038 0.12160354945338636 chrMT 16571 1745 0.1053044475288154 0.3353207868841452 chrX 155270560 3150622 0.02029117432177742 0.1623896023752301 chrY 59373566 170923 0.0028787726848005053 0.08614339925361379