BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818850.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 = 1,830,951 number of mapped reads = 1,805,925 (98.63%) number of supplementary alignments = 29,974 (1.64%) number of secondary alignments = 0 number of mapped bases = 167,128,196 bp number of sequenced bases = 167,023,067 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 450,195 duplication rate = 21.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.262 >>>>>>> ACTG content number of A's = 46,621,874 bp (27.91%) number of C's = 36,819,686 bp (22.04%) number of T's = 48,476,743 bp (29.02%) number of G's = 35,102,203 bp (21.02%) number of N's = 2,561 bp (0%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,012,201 number of insertions = 24,201 mapped reads with insertion percentage = 1.3% number of deletions = 55,063 mapped reads with deletion percentage = 2.98% homopolymer indels = 41.11% >>>>>>> Coverage mean coverageData = 0.054X std coverageData = 0.6272X There is a 3.58% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 15847687 0.06358133406616467 0.9436637181356772 chr2 243199373 12719906 0.05230237990786268 0.9590041723367226 chr3 198022430 10447055 0.052756927586435534 0.3162192377427925 chr4 191154276 8486568 0.04439643296287026 0.3646394605479087 chr5 180915260 7423383 0.04103237615223835 0.30095201659023546 chr6 171115067 8333964 0.04870385843930389 0.33297659464584645 chr7 159138663 15091787 0.09483419500640143 1.2999287170503644 chr8 146364022 14668896 0.10022200674425304 0.5588280510381811 chr9 141213431 6151837 0.04356410687309198 0.5184095033033487 chr10 135534747 7668836 0.056582065999650995 0.7915640222178887 chr11 135006516 7149669 0.052957955007149435 0.3861617605050178 chr12 133851895 6573611 0.049111079077363826 0.3099250560740372 chr13 115169878 5146195 0.04468351525040254 0.2898494013863775 chr14 107349540 4987693 0.046462173941313585 0.3193503446445743 chr15 102531392 4563131 0.04450472105167557 0.29131428860098846 chr16 90354753 4131316 0.04572328364397167 0.6386684596018819 chr17 81195210 4088838 0.050358118416098684 0.40352150715421053 chr18 78077248 3209684 0.04110908212338631 0.6090012888029341 chr19 59128983 2837276 0.04798452224351635 0.7593458907904019 chr20 63025520 6819996 0.10821007109501041 0.4922550410185224 chr21 48129895 1586389 0.03296057471141377 0.3121129402128879 chr22 51304566 1488841 0.029019658796061155 0.2692396468739633 chrMT 16571 250785 15.13396898195643 9.693258369574338 chrX 155270560 6861482 0.04419048916935702 0.34792790707723437 chrY 59373566 593371 0.0099938582095608 0.7062096959505343