BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525244.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 = 1,406,697 number of mapped reads = 1,294,951 (92.06%) number of supplementary alignments = 4,328 (0.31%) number of secondary alignments = 0 number of mapped bases = 75,447,418 bp number of sequenced bases = 75,423,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,388 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1646 >>>>>>> ACTG content number of A's = 18,182,833 bp (24.11%) number of C's = 13,164,715 bp (17.45%) number of T's = 25,235,381 bp (33.46%) number of G's = 18,838,613 bp (24.98%) number of N's = 1,565 bp (0%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 377,210 number of insertions = 5,224 mapped reads with insertion percentage = 0.4% number of deletions = 15,204 mapped reads with deletion percentage = 1.17% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.242X There is a 2.23% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 8656336 0.03472944607026676 0.4111933778183811 chr2 243199373 6014254 0.024729726585273722 0.30509355426260304 chr3 198022430 6121497 0.030913149586135266 0.1905294837564968 chr4 191154276 4152175 0.021721590993862987 0.16571157648382268 chr5 180915260 3371955 0.018638311660387298 0.14600178942259406 chr6 171115067 4667035 0.027274249321364553 0.1944165299265853 chr7 159138663 5205462 0.03271022831202245 0.40767856959563 chr8 146364022 4250000 0.029037190574060612 0.23568075903384983 chr9 141213431 2472637 0.017509927933129818 0.17668634544181464 chr10 135534747 3988876 0.029430652200206638 0.2686948328309571 chr11 135006516 3359600 0.024884724823207794 0.19802249225692017 chr12 133851895 3393866 0.02535538252932467 0.17214671645535745 chr13 115169878 2257484 0.01960134055191063 0.15127674522321816 chr14 107349540 2717262 0.025312283592458802 0.17472406546526362 chr15 102531392 2010598 0.019609584545579952 0.15348706051295738 chr16 90354753 2011708 0.02226455093070754 0.17033542579951103 chr17 81195210 1689375 0.020806338206404047 0.15748037633558182 chr18 78077248 1570332 0.020112542901102252 0.3263070063960527 chr19 59128983 1308425 0.02212831903433888 0.27936678517315217 chr20 63025520 1336385 0.02120387106683134 0.15797257317838628 chr21 48129895 944025 0.019614108861031175 0.15805964485737614 chr22 51304566 628187 0.01224427081207548 0.1181199311245159 chrMT 16571 142390 8.5927222255748 5.12204334233476 chrX 155270560 2980248 0.019193902565946823 0.16039549063769049 chrY 59373566 197306 0.0033231286798572953 0.10376861376266011