BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819067.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,528,941 number of mapped reads = 2,328,130 (92.06%) number of supplementary alignments = 9,528 (0.38%) number of secondary alignments = 0 number of mapped bases = 134,714,190 bp number of sequenced bases = 134,679,428 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,727 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0018 >>>>>>> ACTG content number of A's = 32,442,821 bp (24.09%) number of C's = 26,072,142 bp (19.36%) number of T's = 41,984,871 bp (31.17%) number of G's = 34,176,669 bp (25.38%) number of N's = 2,925 bp (0%) GC percentage = 44.73% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 653,217 number of insertions = 7,927 mapped reads with insertion percentage = 0.34% number of deletions = 20,387 mapped reads with deletion percentage = 0.87% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.0435X std coverageData = 0.3049X There is a 3.78% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 15011092 0.06022489308060741 0.4726533809285269 chr2 243199373 11225074 0.04615585090344785 0.3457813170036009 chr3 198022430 8837448 0.04462852011259533 0.23767184253530751 chr4 191154276 8572039 0.04484356394936203 0.25781307688217436 chr5 180915260 6934285 0.03832891155781994 0.22281896030362064 chr6 171115067 7098580 0.04148424872486536 0.2500501509110378 chr7 159138663 5752991 0.036150806419681936 0.2657434973729368 chr8 146364022 8664726 0.05919983532565127 0.32967907142536074 chr9 141213431 4888672 0.034619029970314935 0.30543041357598727 chr10 135534747 6344367 0.04680989296420054 0.31757252186130824 chr11 135006516 5254467 0.0389200992343214 0.317521996132348 chr12 133851895 6047760 0.04518247575053009 0.24390048711157783 chr13 115169878 4217762 0.036622093148349084 0.21282745614195686 chr14 107349540 3646394 0.033967486027420335 0.2271603857244793 chr15 102531392 3840968 0.03746138548474988 0.21867899603550467 chr16 90354753 3930913 0.04350532616695881 0.2595626037649137 chr17 81195210 2995237 0.036889331279517594 0.2304574375847492 chr18 78077248 3387980 0.04339266670874465 0.5763381756194116 chr19 59128983 2518995 0.04260169670092245 0.35841115261999495 chr20 63025520 4336521 0.06880579485897141 0.3061616443434274 chr21 48129895 1766597 0.03670477569086739 0.23867133030050602 chr22 51304566 1583834 0.03087120939684004 0.19739401595962663 chrMT 16571 13122 0.7918653068613843 1.00835755177798 chrX 155270560 7485919 0.048212095068118514 0.28258681682237613 chrY 59373566 358447 0.00603714791191757 0.13126180746809246