BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089593.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 25,130,779 number of mapped reads = 21,642,471 (86.12%) number of supplementary alignments = 898 (0%) number of secondary alignments = 0 number of mapped bases = 1,017,309,533 bp number of sequenced bases = 1,017,105,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,002,178 duplication rate = 6.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8775 >>>>>>> ACTG content number of A's = 312,648,557 bp (30.74%) number of C's = 205,564,426 bp (20.21%) number of T's = 274,744,482 bp (27.01%) number of G's = 223,878,564 bp (22.01%) number of N's = 269,954 bp (0.03%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 4,472,842 number of insertions = 42,203 mapped reads with insertion percentage = 0.19% number of deletions = 134,909 mapped reads with deletion percentage = 0.62% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.3286X std coverageData = 1.8975X There is a 17.97% of reference with a coverageData >= 1X There is a 6.99% of reference with a coverageData >= 2X There is a 3.17% of reference with a coverageData >= 3X There is a 1.61% of reference with a coverageData >= 4X There is a 0.9% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 81959969 0.3288255358047834 3.3444922899516634 chr2 243199373 84480022 0.3473694070749105 2.0545909220994423 chr3 198022430 67147233 0.33908902642998573 0.9914377502359222 chr4 191154276 67416044 0.35267871276915613 1.1867494878241858 chr5 180915260 61800749 0.34160053165222215 1.011193170942483 chr6 171115067 58593912 0.3424240368032582 1.2502250012992897 chr7 159138663 54431493 0.34203814443256947 2.376455269351629 chr8 146364022 51637572 0.3528023573990062 3.5732323406083326 chr9 141213431 42358940 0.29996396022698435 1.6566571302710822 chr10 135534747 48243083 0.3559462356911324 2.0093976712681636 chr11 135006516 46761085 0.34636168968318537 1.612608265979858 chr12 133851895 46925259 0.3505759780240691 1.0798422954005904 chr13 115169878 32399064 0.28131543214797883 0.8949598310214828 chr14 107349540 30650647 0.2855219221246779 1.1612931690855313 chr15 102531392 28994983 0.2827912743055317 0.9029069351717215 chr16 90354753 28439405 0.31475272806069204 1.1549333031907483 chr17 81195210 26995131 0.33247196478708535 1.2351374337131706 chr18 78077248 26907932 0.3446321776095387 2.845252198398067 chr19 59128983 20557346 0.3476695345834039 2.7770176304484444 chr20 63025520 21404704 0.3396196334437225 1.1118605883004458 chr21 48129895 13235130 0.2749877181323583 1.2605473926999293 chr22 51304566 11441438 0.22301013130098402 0.8087346314905642 chrMT 16571 271124 16.361354172952748 13.01116264795636 chrX 155270560 61093655 0.39346579931185927 1.399227119492321 chrY 59373566 3163613 0.05328319003106534 0.8849021530518704