Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F50 I1 R2	870	341.9	11209456	97.2%	10895591	138.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP025268	390,887	G→A	A356V (GCG→GTG)	CXP41_RS02035 ←	IS3‑like element IS3 family transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP025268	390,887	0	G	A	81.2%	12.3 / ‑3.9	16	A356V (GCG→GTG)	CXP41_RS02035	IS3‑like element IS3 family transposase
Reads supporting (aligned to +/- strand): ref base G (1/2); new base A (12/1); total (13/3)
Fisher's exact test for biased strand distribution p-value = 7.14e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGCCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATACTTCCACG  >  NZ_CP025268/390751‑391014

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGTCTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  1:1129614/1‑140 (MQ=255)

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  1:1888743/1‑140 (MQ=9)

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  1:1953485/1‑140 (MQ=18)

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  1:3538698/1‑140 (MQ=12)

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  1:4181596/1‑140 (MQ=12)

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  1:5341277/1‑140 (MQ=12)

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  2:1111497/1‑140 (MQ=9)

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  2:1112598/1‑140 (MQ=12)

ggggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGCTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCg                                                                                                                              >  2:1109759/1‑140 (MQ=255)

  ggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGtt                                                                                                                            <  1:4263188/140‑1 (MQ=2)

  ggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGtt                                                                                                                            >  2:1324427/1‑140 (MQ=0)

  ggCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTGCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGtt                                                                                                                            >  2:11203/1‑140 (MQ=9)

  ggCTGATTGATCATACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGtt                                                                                                                            >  2:5515345/1‑140 (MQ=0)

                                     gcctAAGCGAGGTTATTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACCCTAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGCCGTTGCCCGCATTATTTCCCGGCTGCTAGAGTGTtcgtc                                                                                         >  2:4080567/4‑137 (MQ=11)

                                                                                agtcatacCAACTGTGCCGCCCCAACCGATTGTAATCACATTCGATATAATTAAACGCCGTTGCCCGCATTATTTCCCGGCTGATAAAGTTTTCTCCATGGATTCATTCCACTTTCAGCATATGAATGAAGCTTTCCACg                                              <  2:644016/134‑1 (MQ=11)

                                                                                                                            agataATTAAAGGCCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACAGTCCACTTTCAGCGAATGAAAGAAGCGTTCCACGCAGGCAGTATCGTAGCAGCAACCTTTTGCGCTCATACTTCCACg  <  2:5345041/138‑1 (MQ=11)

GGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGCCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATACTTCCACG  >  NZ_CP025268/390751‑391014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

AATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGCCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATACTTCCACGCAGATTATGCC  >  NZ_CP025268/390737‑391025

AATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTATGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACA                                                                                                                                            >  SRR14920167.5114531/1‑151 (MQ=43)

 ATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACAC                                                                                                                                           <  SRR14920167.5204125/151‑1 (MQ=39)

 ATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACAC                                                                                                                                           <  SRR14920167.5208558/151‑1 (MQ=39)

 ATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACAC                                                                                                                                           <  SRR14920167.4114595/151‑1 (MQ=39)

   CTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGTCTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCG                                                                                                                                         >  SRR14920167.1131907/1‑151 (MQ=30)

   CTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCG                                                                                                                                         >  SRR14920167.1892626/1‑151 (MQ=31)

   CTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCG                                                                                                                                         >  SRR14920167.1957530/1‑151 (MQ=31)

   CTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCG                                                                                                                                         >  SRR14920167.4190911/1‑151 (MQ=31)

   CTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCG                                                                                                                                         >  SRR14920167.3546454/1‑151 (MQ=31)

   CTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCG                                                                                                                                         >  SRR14920167.5353313/1‑151 (MQ=31)

        GGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCC                                                                                                                                    >  SRR14920167.1874817/1‑151 (MQ=18)

        GGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCC                                                                                                                                    >  SRR14920167.191551/1‑151 (MQ=18)

        GGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCC                                                                                                                                    >  SRR14920167.191597/1‑151 (MQ=18)

        GGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAAAACCGTTGCC                                                                                                                                    <  SRR14920167.3681893/151‑1 (MQ=18)

        GGGTGGGGGGCGGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGGTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCC                                                                                                                                    >  SRR14920167.1874853/1‑151 (MQ=1)

         GGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC                                                                                                                                   <  SRR14920167.2649396/151‑1 (MQ=16)

         GGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC                                                                                                                                   >  SRR14920167.1188383/1‑151 (MQ=16)

         GGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC                                                                                                                                   <  SRR14920167.166952/151‑1 (MQ=16)

          GTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCTGCCACCGATTGTAATCACATTTGATATAATTAAACACCGTTGCCCG                                                                                                                                  >  SRR14920167.1327124/1‑151 (MQ=9)

          GTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCG                                                                                                                                  >  SRR14920167.1523945/1‑151 (MQ=9)

          GTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCG                                                                                                                                  >  SRR14920167.2476061/1‑151 (MQ=9)

          GTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGATCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCG                                                                                                                                  >  SRR14920167.2379722/1‑151 (MQ=9)

              GGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATT                                                                                                                              >  SRR14920167.624981/1‑151 (MQ=0)

               GGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTA                                                                                                                             >  SRR14920167.3556003/1‑151 (MQ=0)

                GGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTAT                                                                                                                            <  SRR14920167.4272672/151‑1 (MQ=0)

                                                                                                                                          ATATAATTAAACCCCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATACTTCCACGCAGATTATGCC  <  SRR14920167.1160741/151‑1 (MQ=0)

AATCTACTGGGTGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACGCCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATACTTCCACGCAGATTATGCC  >  NZ_CP025268/390737‑391025

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`