BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926955.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 10,747,364 number of mapped reads = 10,348,892 (96.29%) number of supplementary alignments = 323,463 (3.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,184,387 number of mapped paired reads (second in pair) = 5,164,505 number of mapped paired reads (both in pair) = 10,168,216 number of mapped paired reads (singletons) = 180,676 number of mapped bases = 942,675,607 bp number of sequenced bases = 941,951,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 674,493 duplication rate = 5.44% >>>>>>> Insert size mean insert size = 311,015.008 std insert size = 5,373,996.237 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 52.714 >>>>>>> ACTG content number of A's = 266,946,758 bp (28.34%) number of C's = 185,960,636 bp (19.74%) number of T's = 269,667,627 bp (28.63%) number of G's = 219,326,852 bp (23.28%) number of N's = 49,211 bp (0.01%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 9,435,655 number of insertions = 161,905 mapped reads with insertion percentage = 1.54% number of deletions = 493,195 mapped reads with deletion percentage = 4.64% homopolymer indels = 52.38% >>>>>>> Coverage mean coverageData = 0.3045X std coverageData = 1.1926X There is a 17.62% of reference with a coverageData >= 1X There is a 6.98% of reference with a coverageData >= 2X There is a 2.84% of reference with a coverageData >= 3X There is a 1.31% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 71020246 0.2849350814656546 1.3240301878557728 chr2 243199373 72877014 0.29965954723082283 1.914821778928008 chr3 198022430 57351539 0.2896214282392151 0.7798731737523561 chr4 191154276 50466744 0.26401054193524814 1.1233746862260858 chr5 180915260 50208500 0.27752495837001256 0.7608081253670766 chr6 171115067 48418041 0.2829560356599107 0.811817689801186 chr7 159138663 85453047 0.5369722567042052 1.2741526787060529 chr8 146364022 41775450 0.2854215771687389 0.8581849911131638 chr9 141213431 35864258 0.2539720035553842 1.2480095810577991 chr10 135534747 40976803 0.3023343010335202 1.5708371014434543 chr11 135006516 40002745 0.2963023281039265 1.0101643362736665 chr12 133851895 38236462 0.28566246297820436 1.3138383347601836 chr13 115169878 25403573 0.2205748016855588 0.6778604453609011 chr14 107349540 25553977 0.2380445878016804 0.7202010972724239 chr15 102531392 25628656 0.24995911496061615 0.7475832209903305 chr16 90354753 49878827 0.5520332394688744 1.3241892492121365 chr17 81195210 22782536 0.2805896554735187 0.8147103871446519 chr18 78077248 43285184 0.5543892120787863 1.6692723279803805 chr19 59128983 14587755 0.24671073743987784 0.9584483490413686 chr20 63025520 20262136 0.32149097698836915 0.8695421925955303 chr21 48129895 10937878 0.22725746648730483 1.1883701033589829 chr22 51304566 22214364 0.43298999936964677 1.12578695162307 chrMT 16571 1248859 75.3641301068131 81.34614252583832 chrX 155270560 46673090 0.3005920117760894 0.823382140604864 chrY 59373566 1567923 0.026407761999675074 0.8094702620929258