BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818810.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,129,659 number of mapped reads = 2,080,047 (97.67%) number of supplementary alignments = 15,839 (0.74%) number of secondary alignments = 0 number of mapped bases = 141,485,763 bp number of sequenced bases = 141,426,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 972,605 duplication rate = 40.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9583 >>>>>>> ACTG content number of A's = 41,019,235 bp (29%) number of C's = 28,955,641 bp (20.47%) number of T's = 39,804,961 bp (28.15%) number of G's = 31,637,912 bp (22.37%) number of N's = 8,427 bp (0.01%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 714,019 number of insertions = 16,077 mapped reads with insertion percentage = 0.76% number of deletions = 36,441 mapped reads with deletion percentage = 1.73% homopolymer indels = 40.31% >>>>>>> Coverage mean coverageData = 0.0457X std coverageData = 0.5455X There is a 2.08% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 11751952 0.04714913829642976 0.7398048321075998 chr2 243199373 12453489 0.05120691244545273 0.9036016410823587 chr3 198022430 9529628 0.0481239827225633 0.4043284865392475 chr4 191154276 9332137 0.0488199228145961 0.47330248233898514 chr5 180915260 8860096 0.04897373499615234 0.42491838463468923 chr6 171115067 8390021 0.049031456709770625 0.4606056602167524 chr7 159138663 7798106 0.049001957494138305 0.48384073389116256 chr8 146364022 7194071 0.049151908383605364 0.46829963563804655 chr9 141213431 6095751 0.04316693502050807 0.45567685826941906 chr10 135534747 6794460 0.050130760933209256 0.5547347037319423 chr11 135006516 6670273 0.049407044916261675 0.46406208535937954 chr12 133851895 6503789 0.04858944283157142 0.4329139175836396 chr13 115169878 4538297 0.03940524274932374 0.3658892779087702 chr14 107349540 4362970 0.040642652031857796 0.4319006947807815 chr15 102531392 4146150 0.04043785926557985 0.37212820104921623 chr16 90354753 4232641 0.046844696703448464 0.6332634663448367 chr17 81195210 3743703 0.046107436633269376 0.41642737082600273 chr18 78077248 3803246 0.048711322407265174 0.571558437817702 chr19 59128983 2796238 0.047290480203253285 0.6778186725919099 chr20 63025520 3055817 0.04848539131450244 0.431001850381229 chr21 48129895 1903559 0.03955044988151335 0.38605366728325435 chr22 51304566 1743076 0.03397506568908506 0.37598216156638736 chrMT 16571 119096 7.187013457244584 7.762662849132124 chrX 155270560 4351652 0.028026253012805518 0.3479044465699893 chrY 59373566 1315545 0.02215708249694822 0.8983104530114245