BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004056.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 = 2,296,683 number of mapped reads = 2,037,938 (88.73%) number of supplementary alignments = 12,097 (0.53%) number of secondary alignments = 0 number of mapped bases = 136,067,498 bp number of sequenced bases = 136,010,171 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,685 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3612 >>>>>>> ACTG content number of A's = 37,293,394 bp (27.42%) number of C's = 25,603,602 bp (18.82%) number of T's = 42,390,316 bp (31.17%) number of G's = 30,713,084 bp (22.58%) number of N's = 9,775 bp (0.01%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,166,692 number of insertions = 9,759 mapped reads with insertion percentage = 0.47% number of deletions = 32,916 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.3646X There is a 3.79% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 10210717 0.040965663230985494 0.6316096729110243 chr2 243199373 10822946 0.04450235979843583 0.44242731310831757 chr3 198022430 9553422 0.048244140827885 0.245459406454115 chr4 191154276 9368473 0.04901001011350643 0.25687925336881035 chr5 180915260 6967739 0.03851382686015541 0.22035429421524505 chr6 171115067 7889092 0.046104017245892207 0.2663846245124833 chr7 159138663 8438481 0.05302596390419593 0.558291288314287 chr8 146364022 9046665 0.06180934956816095 0.4264003090820378 chr9 141213431 3979196 0.02817859442845773 0.3198984683252983 chr10 135534747 7027771 0.05185217190098123 0.3320227063034869 chr11 135006516 5935974 0.04396805558629481 0.31351096240492776 chr12 133851895 6416797 0.04793953047881765 0.25021739194165793 chr13 115169878 4662035 0.04047963826096959 0.23753429953483432 chr14 107349540 3490756 0.032517661463663465 0.2185682011396825 chr15 102531392 3893698 0.0379756670035261 0.22504767212338866 chr16 90354753 3451822 0.03820299304011157 0.24139209433090478 chr17 81195210 3179912 0.039163788110160684 0.23439437148180134 chr18 78077248 4530271 0.05802293390258837 0.6125226210944525 chr19 59128983 2296807 0.03884401326503451 0.47016522573212866 chr20 63025520 3237260 0.05136427275808276 0.26761376061544134 chr21 48129895 1420751 0.029519096187515057 0.20810565516552318 chr22 51304566 1527820 0.029779415734654105 0.19164338257440794 chrMT 16571 87344 5.270894936938024 3.7433692764760127 chrX 155270560 8311057 0.05352628985172721 0.28740551094036826 chrY 59373566 320692 0.005401258869982645 0.10300083780451463