BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006431.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 2,373,121 number of mapped reads = 2,167,204 (91.32%) number of supplementary alignments = 5,620 (0.24%) number of secondary alignments = 0 number of mapped bases = 122,678,362 bp number of sequenced bases = 122,642,880 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,042 duplication rate = 4.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0198 >>>>>>> ACTG content number of A's = 34,949,540 bp (28.5%) number of C's = 25,451,497 bp (20.75%) number of T's = 35,295,804 bp (28.78%) number of G's = 26,943,945 bp (21.97%) number of N's = 2,094 bp (0%) GC percentage = 42.72% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 508,947 number of insertions = 7,524 mapped reads with insertion percentage = 0.35% number of deletions = 21,017 mapped reads with deletion percentage = 0.96% homopolymer indels = 44.48% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.3324X There is a 3.25% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9795476 0.039299705496019605 0.3715898319814404 chr2 243199373 10545320 0.04336080257904283 0.2930400179977389 chr3 198022430 8685193 0.043859642566753676 0.24593221586302674 chr4 191154276 8269493 0.043260831894757094 0.26477657462149556 chr5 180915260 7710773 0.042620909922137025 0.24274721708305264 chr6 171115067 7257679 0.042414026580137446 0.2557201553844261 chr7 159138663 6887125 0.043277509501258034 0.3033010622067103 chr8 146364022 6455547 0.04410610552913065 0.753593515953605 chr9 141213431 5174987 0.03664656373939388 0.2621209313584501 chr10 135534747 5731474 0.04228785700245562 0.32303443448278457 chr11 135006516 5642387 0.04179344202912399 0.2619646865667094 chr12 133851895 5521891 0.04125373794670595 0.23807307135817615 chr13 115169878 3841492 0.0333550062456435 0.2164054537541484 chr14 107349540 3835619 0.03573018570922614 0.5771068839374225 chr15 102531392 3537960 0.03450611496623395 0.218301985867858 chr16 90354753 3604137 0.03988873723112275 0.2737682627190923 chr17 81195210 3139723 0.038668820488302204 0.2516055802174943 chr18 78077248 3295305 0.042205701205042474 0.35110588736765386 chr19 59128983 2139582 0.03618499577440728 0.30696381157936764 chr20 63025520 2725880 0.04325041665661783 0.27737794666618365 chr21 48129895 2217128 0.0460655066876834 0.28084623707017686 chr22 51304566 1367220 0.026649090063445815 0.20569868861699211 chrMT 16571 284398 17.16239213083097 12.373041868746999 chrX 155270560 3888958 0.025046332028428313 0.1903268226126016 chrY 59373566 1123615 0.018924499161798704 0.25782793219008826