BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080666.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,463,846 number of mapped reads = 1,296,046 (88.54%) number of supplementary alignments = 8,972 (0.61%) number of secondary alignments = 0 number of mapped bases = 85,142,474 bp number of sequenced bases = 85,103,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,268 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1679 >>>>>>> ACTG content number of A's = 23,095,984 bp (27.14%) number of C's = 15,520,985 bp (18.24%) number of T's = 26,979,288 bp (31.7%) number of G's = 19,504,032 bp (22.92%) number of N's = 3,498 bp (0%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 636,321 number of insertions = 6,557 mapped reads with insertion percentage = 0.5% number of deletions = 23,666 mapped reads with deletion percentage = 1.81% homopolymer indels = 48.27% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2344X There is a 2.44% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% 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 8924524 0.035805423329316396 0.29355453823758487 chr2 243199373 6971052 0.02866393903079676 0.33644445502323683 chr3 198022430 5321882 0.02687514742648093 0.18000263585766074 chr4 191154276 4186949 0.021903506882576876 0.16564066854576756 chr5 180915260 3963149 0.021906106759595624 0.16255531263410314 chr6 171115067 4957911 0.028974134697326216 0.22127201454157144 chr7 159138663 5385112 0.03383911802752798 0.4180913315944946 chr8 146364022 8475607 0.05790772133878638 0.30045418904429666 chr9 141213431 2827763 0.020024745379920696 0.18792853289440012 chr10 135534747 4037932 0.02979259628529059 0.20601550222652523 chr11 135006516 3633380 0.026912626943132137 0.2104335543394702 chr12 133851895 3255213 0.024319513743156194 0.17382933414114476 chr13 115169878 1801626 0.01564320490119821 0.13699283922661354 chr14 107349540 2134099 0.01987990819522841 0.15804217389506756 chr15 102531392 1787351 0.01743223187684802 0.15414609213789668 chr16 90354753 2364519 0.026169281874966775 0.18336611485005844 chr17 81195210 1700363 0.020941666386477726 0.16854839309999728 chr18 78077248 2444137 0.03130408745963997 0.28221630589272767 chr19 59128983 1441162 0.024373191062663804 0.22245744490239228 chr20 63025520 2066482 0.03278801983704379 0.2026673569879298 chr21 48129895 1314338 0.02730814185237678 0.186022754186492 chr22 51304566 786637 0.01533268988183235 0.13636561261558414 chrMT 16571 13434 0.8106933800012069 1.2075200390354797 chrX 155270560 5171895 0.03330892218074051 0.21075783411894852 chrY 59373566 175957 0.0029635578903918288 0.06321868561521087