BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504426.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,038,247 number of mapped reads = 1,787,604 (87.7%) number of secondary alignments = 0 number of mapped bases = 57,197,176 bp number of sequenced bases = 57,197,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 240,735 duplication rate = 6.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.0864 >>>>>>> ACTG content number of A's = 16,427,893 bp (28.72%) number of C's = 11,641,679 bp (20.35%) number of T's = 17,652,474 bp (30.86%) number of G's = 11,475,009 bp (20.06%) number of N's = 121 bp (0%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0006 number of mismatches = 32,727 >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.7284X There is a 1.15% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 4985390 0.020001514860819546 0.43895117539650375 chr2 243199373 4782592 0.019665313857532025 0.2634942040285379 chr3 198022430 5311838 0.026824425899631674 0.8236169359428434 chr4 191154276 3747802 0.01960616355764911 0.33085635370005434 chr5 180915260 3547730 0.019609899131781367 0.1984040061888955 chr6 171115067 3118532 0.018224765677706218 0.42343387674430666 chr7 159138663 3993706 0.025095761926817242 1.799552512749914 chr8 146364022 3217274 0.021981317239287125 0.7201407932400107 chr9 141213431 2451002 0.017356720126713725 0.4039962952664091 chr10 135534747 3047206 0.02248283976949468 0.6422970737084444 chr11 135006516 2939514 0.02177312686152126 1.069841129207838 chr12 133851895 2420958 0.018086841430224054 0.2985473936237247 chr13 115169878 1676890 0.014560143929300681 0.30390671378571266 chr14 107349540 1510578 0.01407158335284902 0.16717925117615173 chr15 102531392 1912890 0.01865662762093389 0.45973972372720845 chr16 90354753 1703690 0.01885556590476209 1.3069200673705808 chr17 81195210 781720 0.009627661533235765 0.1276142331623709 chr18 78077248 1098700 0.014071961142892742 0.33653624575245294 chr19 59128983 760942 0.012869188025777478 0.42281419499039186 chr20 63025520 764448 0.012129181956769259 0.1900269128016964 chr21 48129895 542094 0.011263145286313215 0.2525107256319956 chr22 51304566 1260454 0.024568066709695975 2.3017989284224694 chrMT 16571 2622 0.15822823004043207 0.3926736563307992 chrX 155270560 735714 0.004738271054087781 0.08385331193716612 chrY 59373566 882890 0.014870085451832217 0.9972783810711972