BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068142.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 = 2,597,138
number of mapped reads = 2,370,050 (91.26%)
number of supplementary alignments = 18,557 (0.71%)
number of secondary alignments = 0
number of mapped bases = 146,733,448 bp
number of sequenced bases = 146,662,422 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 965,909
duplication rate = 23.72%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.1703
>>>>>>> ACTG content
number of A's = 36,856,816 bp (25.13%)
number of C's = 25,088,581 bp (17.11%)
number of T's = 49,419,624 bp (33.7%)
number of G's = 35,282,452 bp (24.06%)
number of N's = 14,949 bp (0.01%)
GC percentage = 41.16%
>>>>>>> Mismatches and indels
general error rate = 0.0067
number of mismatches = 957,759
number of insertions = 9,637
mapped reads with insertion percentage = 0.4%
number of deletions = 40,558
mapped reads with deletion percentage = 1.69%
homopolymer indels = 47.19%
>>>>>>> Coverage
mean coverageData = 0.0474X
std coverageData = 0.7435X
There is a 1.41% of reference with a coverageData >= 1X
There is a 0.87% of reference with a coverageData >= 2X
There is a 0.64% of reference with a coverageData >= 3X
There is a 0.46% of reference with a coverageData >= 4X
There is a 0.33% of reference with a coverageData >= 5X
There is a 0.23% of reference with a coverageData >= 6X
There is a 0.16% of reference with a coverageData >= 7X
There is a 0.12% of reference with a coverageData >= 8X
There is a 0.08% of reference with a coverageData >= 9X
There is a 0.06% of reference with a coverageData >= 10X
There is a 0.05% of reference with a coverageData >= 11X
There is a 0.03% of reference with a coverageData >= 12X
There is a 0.03% of reference with a coverageData >= 13X
There is a 0.02% of reference with a coverageData >= 14X
There is a 0.02% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% 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 15070520 0.060463319768418955 0.9664571296162783
chr2 243199373 12529300 0.05151863611095741 1.0658182693113298
chr3 198022430 10903484 0.05506186344647927 0.729247659784356
chr4 191154276 7958006 0.04163132610227354 0.6472463529757446
chr5 180915260 6588881 0.036419708320901176 0.5287718699839802
chr6 171115067 10513916 0.06144354313346352 0.7360064891759136
chr7 159138663 10598883 0.06660155866711033 0.9122471720063183
chr8 146364022 6194910 0.0423253605315656 0.8026282041594615
chr9 141213431 4946022 0.035025152812836906 0.6215126687204059
chr10 135534747 7583305 0.0559510027343763 0.6749790735084568
chr11 135006516 6498891 0.04813760989136258 0.6646941129601409
chr12 133851895 6346640 0.04741539146681487 0.5970753307778499
chr13 115169878 3802220 0.0330140143067617 0.558857368350909
chr14 107349540 3653563 0.03403426786924285 0.5162388564971684
chr15 102531392 3290887 0.03209638468577507 0.5600852070873688
chr16 90354753 3567716 0.0394856483089495 0.573491542379161
chr17 81195210 4242568 0.052251456705389394 0.6084815274074512
chr18 78077248 3549016 0.04545518817466517 1.135765894948935
chr19 59128983 3324572 0.056225759878197126 0.7903365446785282
chr20 63025520 2366183 0.03754325232064726 0.5620856510375603
chr21 48129895 2460890 0.05113017595405101 0.6471224317185892
chr22 51304566 1697279 0.033082416095284777 0.4857621797913742
chrMT 16571 192420 11.611852030655966 13.39157291689238
chrX 155270560 8361794 0.05385305495130564 0.6607573387171006
chrY 59373566 491582 0.008279475751885949 0.23715392584526526