BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008662.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 = 1,915,433 number of mapped reads = 1,589,806 (83%) number of supplementary alignments = 14,104 (0.74%) number of secondary alignments = 0 number of mapped bases = 103,433,732 bp number of sequenced bases = 103,390,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,492 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4945 >>>>>>> ACTG content number of A's = 27,543,985 bp (26.64%) number of C's = 19,107,265 bp (18.48%) number of T's = 32,611,446 bp (31.54%) number of G's = 24,089,997 bp (23.3%) number of N's = 38,188 bp (0.04%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 846,439 number of insertions = 7,145 mapped reads with insertion percentage = 0.45% number of deletions = 25,585 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 0.3101X There is a 2.74% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.08% 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 9406949 0.0377409250266221 0.5581811639109774 chr2 243199373 11872772 0.04881908967750505 0.38031868854096307 chr3 198022430 7477097 0.03775883873357175 0.22797898039640052 chr4 191154276 8123217 0.04249560705615604 0.24760172359750807 chr5 180915260 4858682 0.026856120373704242 0.19258297489290402 chr6 171115067 4499664 0.02629612972655412 0.20976205223238484 chr7 159138663 5828309 0.03662409178340276 0.49528415774328144 chr8 146364022 3853351 0.026327173490764008 0.28585323011718666 chr9 141213431 2867376 0.020305264022655183 0.23222610334250318 chr10 135534747 6384561 0.047106451602407166 0.34035932868621355 chr11 135006516 3841396 0.02845341183384067 0.24428420304769552 chr12 133851895 5646851 0.042187307097893534 0.24577786850982328 chr13 115169878 2251556 0.01954986875995475 0.16330651443072328 chr14 107349540 3056451 0.02847195246481727 0.2042088333571891 chr15 102531392 2853950 0.027834889825742344 0.2011102783973903 chr16 90354753 3025250 0.03348191323150427 0.22088553200258187 chr17 81195210 2697149 0.033218080229116966 0.23410977497685512 chr18 78077248 2524498 0.03233333736353003 0.3946598490573198 chr19 59128983 2407364 0.0407137731423522 0.3933578557562618 chr20 63025520 1772084 0.02811692787302667 0.20276524326123657 chr21 48129895 1005883 0.02089933917370898 0.17584640882836353 chr22 51304566 775405 0.015113761999273126 0.14152667844337194 chrMT 16571 87367 5.272282903868203 3.7364594785713514 chrX 155270560 6074280 0.03912061629712677 0.2500960964735816 chrY 59373566 242270 0.00408043539106275 0.09498566698958735