BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006436.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 = 1,299,356 number of mapped reads = 1,219,202 (93.83%) number of supplementary alignments = 3,223 (0.25%) number of secondary alignments = 0 number of mapped bases = 67,979,076 bp number of sequenced bases = 67,957,697 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,125 duplication rate = 1.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6567 >>>>>>> ACTG content number of A's = 19,097,865 bp (28.1%) number of C's = 14,503,983 bp (21.34%) number of T's = 18,651,622 bp (27.45%) number of G's = 15,633,530 bp (23%) number of N's = 70,697 bp (0.1%) GC percentage = 44.35% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 378,772 number of insertions = 4,403 mapped reads with insertion percentage = 0.36% number of deletions = 12,427 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.39% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 0.2034X There is a 2% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5622563 0.022557869574976908 0.22657513391380021 chr2 243199373 5607739 0.023058196782439897 0.18321965030572446 chr3 198022430 4468549 0.02256587296701692 0.16065948053039505 chr4 191154276 4228735 0.02212210518377313 0.1656511761733688 chr5 180915260 4041244 0.02233777294408443 0.16020127438756881 chr6 171115067 3876762 0.022655877521293902 0.1657251257352215 chr7 159138663 3833800 0.024090940113025833 0.19038194971037983 chr8 146364022 3422232 0.023381647711211435 0.5054032055364458 chr9 141213431 2869125 0.02031764953009321 0.16260387551845357 chr10 135534747 3267401 0.024107478505124593 0.1858128943666285 chr11 135006516 3209127 0.023770163804538145 0.17527833698929934 chr12 133851895 3082647 0.023030282836115246 0.16350875031007153 chr13 115169878 2135831 0.018545048732273556 0.14649536948229663 chr14 107349540 2114899 0.01970105321364209 0.15301153118029723 chr15 102531392 2024327 0.01974348500018414 0.15160721971173735 chr16 90354753 2168359 0.023998283742748983 0.18314566114595024 chr17 81195210 2047265 0.02521411053681615 0.17749433944178766 chr18 78077248 1787173 0.02288980523493861 0.20269816671419708 chr19 59128983 1606445 0.027168486899225037 0.21724476250799618 chr20 63025520 1589679 0.02522278277116952 0.18532500944122848 chr21 48129895 1273518 0.02646002032624422 0.18769559019580506 chr22 51304566 970086 0.018908375523535272 0.15638386475774532 chrMT 16571 47213 2.849134029328345 2.1961370676715735 chrX 155270560 2082953 0.013414989937564467 0.12664907874147702 chrY 59373566 601404 0.010129154108749337 0.14983111036875835