BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818984.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 = 1,840,396 number of mapped reads = 1,817,568 (98.76%) number of supplementary alignments = 22,565 (1.23%) number of secondary alignments = 0 number of mapped bases = 168,779,208 bp number of sequenced bases = 168,680,546 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 754,118 duplication rate = 35.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3743 >>>>>>> ACTG content number of A's = 48,138,335 bp (28.54%) number of C's = 35,384,309 bp (20.98%) number of T's = 46,302,233 bp (27.45%) number of G's = 38,847,411 bp (23.03%) number of N's = 8,258 bp (0%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,030,986 number of insertions = 22,727 mapped reads with insertion percentage = 1.22% number of deletions = 53,459 mapped reads with deletion percentage = 2.88% homopolymer indels = 42.79% >>>>>>> Coverage mean coverageData = 0.0545X std coverageData = 0.6345X There is a 2.7% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% 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 0.02% 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 0.01% 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 16554690 0.06641784856375543 1.1398757727168405 chr2 243199373 13425445 0.055203452354295336 0.8395459862363355 chr3 198022430 8763870 0.044256956143806536 0.36626623675701114 chr4 191154276 8903766 0.04657895280354597 0.4193120217254771 chr5 180915260 11434181 0.06320186036269135 0.44909509763108396 chr6 171115067 6902440 0.040338002497465636 0.4269269740995891 chr7 159138663 8144650 0.051179580414094594 0.7366660209395373 chr8 146364022 15978953 0.10917268316116648 0.6437588618627964 chr9 141213431 7119538 0.050416861551929856 0.582181898320557 chr10 135534747 8804984 0.06496477246532212 0.7466628700146719 chr11 135006516 5517982 0.040871967987085894 0.4275851342741043 chr12 133851895 7699598 0.05752326479950097 0.4293607755343855 chr13 115169878 3591282 0.031182476376331664 0.3078032702004473 chr14 107349540 3915756 0.03647669100398567 0.3517546813825892 chr15 102531392 4375388 0.042673642819557156 0.36434482169425 chr16 90354753 5363540 0.059360906005686276 0.653722913922677 chr17 81195210 5573903 0.06864817518176257 0.5284167597898501 chr18 78077248 3773600 0.0483316215243652 0.6677739660071546 chr19 59128983 3530318 0.05970537325155753 1.0560385744602716 chr20 63025520 4918048 0.07803264455414251 0.5307907354757446 chr21 48129895 2246599 0.04667782882135937 0.4131228277350755 chr22 51304566 1405562 0.027396430953143626 0.3131617446942339 chrMT 16571 375238 22.644258041156238 14.831408093385381 chrX 155270560 9870536 0.06356991306014483 0.5078515477277461 chrY 59373566 589341 0.009925982886054039 0.5749395440507803