BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6240261.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 = 1,679,679
number of mapped reads = 1,389,662 (82.73%)
number of supplementary alignments = 5,746 (0.34%)
number of secondary alignments = 0
number of mapped bases = 86,215,016 bp
number of sequenced bases = 86,167,675 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 59,923
duplication rate = 3.43%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.4035
>>>>>>> ACTG content
number of A's = 23,296,454 bp (27.04%)
number of C's = 14,905,713 bp (17.3%)
number of T's = 27,408,952 bp (31.81%)
number of G's = 20,536,679 bp (23.83%)
number of N's = 19,877 bp (0.02%)
GC percentage = 41.13%
>>>>>>> Mismatches and indels
general error rate = 0.0096
number of mismatches = 817,402
number of insertions = 6,364
mapped reads with insertion percentage = 0.46%
number of deletions = 27,589
mapped reads with deletion percentage = 1.96%
homopolymer indels = 49.21%
>>>>>>> Coverage
mean coverageData = 0.0278X
std coverageData = 0.2786X
There is a 2.41% of reference with a coverageData >= 1X
There is a 0.28% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% 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 6384402 0.025614387536470773 0.384833221638581
chr2 243199373 10417269 0.042834275728169745 0.36123849541074876
chr3 198022430 5621765 0.028389536478266628 0.19145951707594427
chr4 191154276 5118574 0.02677718807608573 0.1945680422282692
chr5 180915260 4481672 0.024772216561499565 0.18043180322715927
chr6 171115067 4758206 0.02780705453599828 0.23591150552415574
chr7 159138663 5572730 0.03501807728521635 0.5590934064021102
chr8 146364022 4653123 0.03179143983895168 0.3498929930882581
chr9 141213431 2832459 0.020058000007095643 0.23116268770674728
chr10 135534747 4125224 0.030436652528668534 0.23299402161337995
chr11 135006516 3410405 0.02526103999306226 0.22946272368424378
chr12 133851895 4062431 0.030350194145551693 0.1990368495899364
chr13 115169878 1448863 0.012580225187005929 0.12889907559501432
chr14 107349540 3090404 0.028788237005952705 0.2031739615331058
chr15 102531392 2368950 0.02310463121382376 0.1974154859865381
chr16 90354753 3001897 0.03322345422160581 0.21483154973031957
chr17 81195210 2563151 0.0315677612016768 0.21528503419950026
chr18 78077248 1734156 0.0222107725928045 0.3656042387873958
chr19 59128983 1945980 0.032910763914204305 0.293415585120822
chr20 63025520 1769563 0.028076928203051715 0.1949009015965331
chr21 48129895 1556808 0.03234596709591824 0.2113557440398464
chr22 51304566 828365 0.01614602879595551 0.14064944101734533
chrMT 16571 25920 1.5641783839237222 1.763413835928531
chrX 155270560 4260478 0.027439058634167353 0.20925373994700258
chrY 59373566 182221 0.003069059385787945 0.0699996535789788