BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238242.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 = 1,437,016 number of mapped reads = 1,104,816 (76.88%) number of supplementary alignments = 13,687 (0.95%) number of secondary alignments = 0 number of mapped bases = 69,890,734 bp number of sequenced bases = 69,859,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,330 duplication rate = 8.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4647 >>>>>>> ACTG content number of A's = 19,501,326 bp (27.92%) number of C's = 13,773,342 bp (19.72%) number of T's = 21,122,369 bp (30.24%) number of G's = 15,442,048 bp (22.1%) number of N's = 20,504 bp (0.03%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 629,909 number of insertions = 5,420 mapped reads with insertion percentage = 0.49% number of deletions = 19,237 mapped reads with deletion percentage = 1.72% homopolymer indels = 45.43% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.3021X There is a 1.43% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 4918605 0.0197335716968986 0.39694558449191913 chr2 243199373 8196820 0.033704116498688506 0.4443635754034748 chr3 198022430 3618466 0.018273010789737303 0.20365781692390128 chr4 191154276 4781437 0.025013497474678514 0.24717184308607806 chr5 180915260 5656847 0.031267937265214665 0.270765693809914 chr6 171115067 4493975 0.026262883092580035 0.2764656508836075 chr7 159138663 4291199 0.02696515679536657 0.3966885220937214 chr8 146364022 3315480 0.02265228814223211 0.3268288337204217 chr9 141213431 2223358 0.015744663834419546 0.2548581140716504 chr10 135534747 2528512 0.018655821152637708 0.2609405837240178 chr11 135006516 1658903 0.012287577289973175 0.18359099323666964 chr12 133851895 5749259 0.04295239152198779 0.32381015175524297 chr13 115169878 1240747 0.010773190191275536 0.1873948937085495 chr14 107349540 1448540 0.01349367682432547 0.3057805107084807 chr15 102531392 1855349 0.018095423887349544 0.38363083203682524 chr16 90354753 2343685 0.025938701863309835 0.24220960134202899 chr17 81195210 1898736 0.023384827750306945 0.24190142892448463 chr18 78077248 2158411 0.027644557861465607 0.34809924084253 chr19 59128983 1187527 0.02008367030429054 0.3138703695319364 chr20 63025520 2142857 0.03399983054483327 0.27817268275446105 chr21 48129895 572507 0.011895039455207621 0.1613093003168398 chr22 51304566 890510 0.017357324492326864 0.19853042876885257 chrMT 16571 15941 0.9619817753907428 1.4589838575372494 chrX 155270560 2548880 0.01641573264113944 0.22755185924746527 chrY 59373566 154183 0.0025968290333108846 0.08531160909023992