BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234123.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 = 3,425,594 number of mapped reads = 3,155,698 (92.12%) number of supplementary alignments = 35,046 (1.02%) number of secondary alignments = 0 number of mapped bases = 216,309,781 bp number of sequenced bases = 216,241,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 527,172 duplication rate = 6.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2188 >>>>>>> ACTG content number of A's = 54,942,080 bp (25.41%) number of C's = 37,888,603 bp (17.52%) number of T's = 59,411,166 bp (27.47%) number of G's = 63,953,727 bp (29.58%) number of N's = 46,313 bp (0.02%) GC percentage = 47.1% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,316,112 number of insertions = 14,447 mapped reads with insertion percentage = 0.45% number of deletions = 41,853 mapped reads with deletion percentage = 1.31% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 0.0699X std coverageData = 42.4913X There is a 3.71% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.25% 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 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 13865370 0.055628226498982324 0.6783262974853297 chr2 243199373 39475687 0.1623182104174257 151.58762774246935 chr3 198022430 12772270 0.06449910750009481 0.39230341919946354 chr4 191154276 12693161 0.06640270500671405 0.41154082603139436 chr5 180915260 12179733 0.06732286154302296 0.4033039870588929 chr6 171115067 13385584 0.07822563047589491 0.5242287864114151 chr7 159138663 10970173 0.06893468119686288 0.8869155281919012 chr8 146364022 9971698 0.06812943415834802 0.9481798923415564 chr9 141213431 8534927 0.06043990957205763 0.5432512368785957 chr10 135534747 9118557 0.06727837105860389 0.4944437161038618 chr11 135006516 8644566 0.06403073167224017 0.5620786181196045 chr12 133851895 8072102 0.060306221290329885 0.3910529634041445 chr13 115169878 6830764 0.059310334599816106 0.3781026230234831 chr14 107349540 5676615 0.052879732880085004 0.46806204535795953 chr15 102531392 5473244 0.05338115374460146 0.3602931020209439 chr16 90354753 5293813 0.058589203381475684 0.4027269102461119 chr17 81195210 5295012 0.0652133543345722 0.48269749555610725 chr18 78077248 5142256 0.06586113281041872 0.9492112847635926 chr19 59128983 3476314 0.05879204788622865 0.5515927573384938 chr20 63025520 3584087 0.05686723409818753 0.3821945759361228 chr21 48129895 2659245 0.05525141910241026 0.3917389215343482 chr22 51304566 1939905 0.03781154683191356 0.2983456797943008 chrMT 16571 18166 1.0962524892885162 1.4515244497410082 chrX 155270560 10792257 0.06950613818872038 0.4378191054096664 chrY 59373566 444275 0.007482707034979169 0.1753080142500644