BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068169.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 = 1,608,743 number of mapped reads = 1,417,922 (88.14%) number of supplementary alignments = 14,792 (0.92%) number of secondary alignments = 0 number of mapped bases = 96,379,162 bp number of sequenced bases = 96,332,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 163,125 duplication rate = 8.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1403 >>>>>>> ACTG content number of A's = 27,891,887 bp (28.95%) number of C's = 18,260,062 bp (18.96%) number of T's = 30,090,421 bp (31.24%) number of G's = 19,987,225 bp (20.75%) number of N's = 103,195 bp (0.11%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 854,645 number of insertions = 7,433 mapped reads with insertion percentage = 0.52% number of deletions = 26,249 mapped reads with deletion percentage = 1.83% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.4485X There is a 1.38% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 7607190 0.03052024492247905 0.5708776967532618 chr2 243199373 8161384 0.03355840888619396 0.3950058306369863 chr3 198022430 5332604 0.0269292928078905 0.36500759913255904 chr4 191154276 5526153 0.02890938730557092 0.3315481713720655 chr5 180915260 5465659 0.03021115521156148 0.33121858287373884 chr6 171115067 6160021 0.03599929046575425 0.3707886242299645 chr7 159138663 5331090 0.0334996530667095 0.4418072124658995 chr8 146364022 4539238 0.03101334561576888 0.4295824105416945 chr9 141213431 3774071 0.026726005970352778 0.3540614584543442 chr10 135534747 4690109 0.0346044767398282 1.0893718901219693 chr11 135006516 3630346 0.02689015395375435 0.35220253550261993 chr12 133851895 3881172 0.028996018323087618 0.32660703809617864 chr13 115169878 2335619 0.020279773153879698 0.2696434649007574 chr14 107349540 2448785 0.02281132271270096 0.28901010798320287 chr15 102531392 2253324 0.021976918054521292 0.2739397813312341 chr16 90354753 2230389 0.024684799924139023 0.3261254180915878 chr17 81195210 1934773 0.023828659350717856 0.29440628603265007 chr18 78077248 1993271 0.025529473067493362 0.5762018128585753 chr19 59128983 1470807 0.02487455263690228 0.3850311116216048 chr20 63025520 1534453 0.024346534546640788 0.2947464960956273 chr21 48129895 1359934 0.028255494843693302 0.3188501378154344 chr22 51304566 1346739 0.026249885828875347 0.296649623411481 chrMT 16571 104716 6.319232393941222 5.369207330952017 chrX 155270560 13002157 0.08373871389399253 0.57297339951801 chrY 59373566 265158 0.004465926806552263 0.137621575090221