BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504423.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 = 2,271,704 number of mapped reads = 1,962,087 (86.37%) number of secondary alignments = 0 number of mapped bases = 62,780,194 bp number of sequenced bases = 62,780,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,441 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.4705 >>>>>>> ACTG content number of A's = 18,133,601 bp (28.88%) number of C's = 12,438,190 bp (19.81%) number of T's = 19,948,388 bp (31.77%) number of G's = 12,259,853 bp (19.53%) number of N's = 162 bp (0%) GC percentage = 39.34% >>>>>>> Mismatches and indels general error rate = 0.0006 number of mismatches = 39,183 >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.3201X There is a 1.49% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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% 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 4874788 0.01955777674872874 0.21054033229793226 chr2 243199373 5290934 0.021755541285873297 0.2434768377959926 chr3 198022430 4377148 0.0221043040427289 0.2823035173044686 chr4 191154276 3971726 0.020777594323864352 0.19852011430749913 chr5 180915260 4235418 0.023411059962548213 0.2707125911893837 chr6 171115067 3715184 0.021711612338614225 0.27176788311199024 chr7 159138663 3176748 0.01996213830199139 0.21182898195574779 chr8 146364022 4588384 0.03134912485528718 0.92820558709655 chr9 141213431 2244660 0.015895513508201637 0.17931385045718096 chr10 135534747 2418176 0.017841742088469757 0.173955715252115 chr11 135006516 2622458 0.019424677250392864 0.19282932991789292 chr12 133851895 2703544 0.020198025586414 0.21547618669452487 chr13 115169878 2116826 0.018380031625977757 0.21228850098851246 chr14 107349540 2062012 0.019208391577644396 0.18741126694394566 chr15 102531392 1535926 0.014980056059318887 0.1824289505947609 chr16 90354753 1554838 0.017208148419154 0.4519662167045863 chr17 81195210 1161828 0.01430907069518017 0.39543694008653 chr18 78077248 1547382 0.019818603237655098 0.20008384584687258 chr19 59128983 543374 0.009189638861199423 0.11079735563282603 chr20 63025520 1095248 0.01737784948065482 0.1851305112504138 chr21 48129895 864226 0.017956116463582562 0.22639264688034075 chr22 51304566 384688 0.007498124046113166 0.11236479092071246 chrMT 16571 0 0.0 0.0 chrX 155270560 5503588 0.03544514813368355 0.48425378390950036 chrY 59373566 191090 0.0032184356250389273 0.06915232267967325