BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230375.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,894,795 number of mapped reads = 1,557,731 (82.21%) number of supplementary alignments = 19,989 (1.05%) number of secondary alignments = 0 number of mapped bases = 102,216,765 bp number of sequenced bases = 102,165,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,633 duplication rate = 8.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8672 >>>>>>> ACTG content number of A's = 27,884,076 bp (27.29%) number of C's = 19,040,550 bp (18.64%) number of T's = 32,104,257 bp (31.42%) number of G's = 23,117,432 bp (22.63%) number of N's = 18,978 bp (0.02%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 911,449 number of insertions = 8,158 mapped reads with insertion percentage = 0.52% number of deletions = 31,067 mapped reads with deletion percentage = 1.97% homopolymer indels = 45.85% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3652X There is a 1.88% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% 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% 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 8220180 0.03297957680915868 0.5445583156888072 chr2 243199373 2458664 0.01010966422187281 0.3199890072746222 chr3 198022430 2611918 0.01319001084877102 0.20634019493265165 chr4 191154276 3927240 0.020544871305939294 0.23808478433731908 chr5 180915260 10832402 0.059875557208385846 0.3981842500522126 chr6 171115067 6725263 0.03930257643530596 0.351616270764774 chr7 159138663 2541691 0.01597154928969084 0.24027752257638668 chr8 146364022 4967401 0.033938675175242176 0.47423029840833475 chr9 141213431 4667602 0.03305352732347393 0.31231680036731835 chr10 135534747 2819891 0.020805668379636995 0.3825773445197101 chr11 135006516 2830741 0.020967439823423042 0.2537793019946563 chr12 133851895 5938899 0.04436918132537459 0.34352109801159747 chr13 115169878 7404707 0.06429378174734196 0.4101944923811479 chr14 107349540 4797007 0.04468586451325269 0.35724276003133026 chr15 102531392 4038233 0.03938533283543054 0.337319825817099 chr16 90354753 2040674 0.022585131741769026 0.24937744657319205 chr17 81195210 4151641 0.051131600004483024 0.37750101881895304 chr18 78077248 2340897 0.02998180724812432 0.537054167811201 chr19 59128983 3398417 0.05747463980566011 0.47439408168634345 chr20 63025520 1175413 0.01864979455941022 0.23906183565170264 chr21 48129895 2224297 0.04621445777099659 0.35175418208938464 chr22 51304566 1135234 0.022127348275395215 0.2391630055989092 chrMT 16571 9671 0.5836099209462313 1.1459592069599747 chrX 155270560 10691752 0.068858848708989 0.4583833013204162 chrY 59373566 266930 0.004495771737880794 0.12469405126371096