BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524739.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 = 1,650,748 number of mapped reads = 1,504,832 (91.16%) number of supplementary alignments = 5,803 (0.35%) number of secondary alignments = 0 number of mapped bases = 85,712,135 bp number of sequenced bases = 85,684,606 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,583 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5267 >>>>>>> ACTG content number of A's = 20,564,288 bp (24%) number of C's = 15,677,085 bp (18.3%) number of T's = 27,921,046 bp (32.59%) number of G's = 21,512,286 bp (25.11%) number of N's = 9,901 bp (0.01%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 433,421 number of insertions = 6,040 mapped reads with insertion percentage = 0.4% number of deletions = 17,151 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.96% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2519X There is a 2.46% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 6888149 0.027635433654546442 0.35681849431472673 chr2 243199373 7230590 0.029731121058441216 0.3973651646411017 chr3 198022430 5645675 0.028510280375813993 0.18894929689230194 chr4 191154276 5507114 0.028809787127126573 0.21732698042945992 chr5 180915260 5086778 0.028116909540964095 0.18423216132652945 chr6 171115067 4853943 0.02836654354931819 0.20646780703802095 chr7 159138663 4670510 0.029348681910190487 0.2946832790982556 chr8 146364022 4291453 0.029320409082499797 0.23114964008671124 chr9 141213431 3700172 0.0262026917255484 0.22017180738240713 chr10 135534747 4193116 0.030937572045639336 0.3013246190218222 chr11 135006516 3845497 0.028483788145455144 0.21762473078978498 chr12 133851895 3887311 0.02904188244776064 0.19044776729248347 chr13 115169878 2653098 0.023036388038893296 0.16637826724847843 chr14 107349540 2547028 0.02372649198124184 0.17502804947322764 chr15 102531392 2489132 0.024276779544746645 0.1732388332430139 chr16 90354753 2600190 0.02877756746233372 0.2049661840815075 chr17 81195210 2402891 0.029593999448982274 0.2022407849168796 chr18 78077248 2246447 0.028772107848883198 0.33963308906469264 chr19 59128983 1858516 0.031431557008176514 0.30143026015651087 chr20 63025520 1845946 0.02928886584355036 0.19619594561082926 chr21 48129895 1143530 0.023759245682958584 0.1908995605414811 chr22 51304566 1064566 0.020749927014293425 0.16083850863839028 chrMT 16571 11650 0.7030354233299138 1.003525358822627 chrX 155270560 4753930 0.03061707254742947 0.20894424220210941 chrY 59373566 294903 0.004966907327075487 0.15197873225985115