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
A14 F1 I1 R1	71	51.6	2219666	95.9%	2128659	118.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,763,869	(T)_7→8	coding (1285/1617 nt)	yfjL ←	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,763,862	1	.	T	95.9%	162.6 / ‑0.3	49	coding (1292/1617 nt)	yfjL	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
Reads supporting (aligned to +/- strand): ref base . (1/1); new base T (22/25); total (23/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.46e-01

TTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTG  >  NC_000913/2763736‑2763994

ttAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑ttttttttgcgc                                                                                                                          >  2:148326/1‑134 (MQ=255)

ttAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑ttttttttgcgc                                                                                                                          >  1:481840/1‑134 (MQ=255)

 tAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcg                                                                                                                          >  2:302540/1‑139 (MQ=255)

 tAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcg                                                                                                                          >  1:340211/1‑139 (MQ=255)

       cGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTAt                                                                                                                    <  2:481840/139‑1 (MQ=255)

        gTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATc                                                                                                                   >  1:917808/1‑139 (MQ=255)

             ccACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGc                                                                                                              <  2:1012692/139‑1 (MQ=255)

                cGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAAt                                                                                                           <  1:159912/139‑1 (MQ=255)

                           aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                <  2:563343/139‑1 (MQ=255)

                            aCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcgc                                                                                                                         <  1:164147/113‑1 (MQ=255)

                            aCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcgc                                                                                                                         >  2:164147/1‑113 (MQ=255)

                                 aaaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATg                                                                                                   >  2:901869/1‑130 (MQ=255)

                                 aaaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATg                                                                                                   <  1:901869/130‑1 (MQ=255)

                                 aaaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTAc                                                                                          >  1:377309/1‑139 (MQ=255)

                                  aaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACa                                                                                         <  1:414800/139‑1 (MQ=255)

                                   aCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACaa                                                                                        <  2:1066871/139‑1 (MQ=255)

                                               aGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAt                                                                            >  2:31625/1‑139 (MQ=255)

                                                 cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcgc                                                                                                                         >  2:96312/1‑92 (MQ=255)

                                                 cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcgc                                                                                                                         >  2:577153/1‑92 (MQ=255)

                                                 cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcgc                                                                                                                         <  1:96312/92‑1 (MQ=255)

                                                 cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcgc                                                                                                                         <  1:577153/92‑1 (MQ=255)

                                                 cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAtct                                                                          >  1:56092/1‑139 (MQ=255)

                                                 cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAtctc                                                                         >  1:359066/1‑139 (MQ=255)

                                                      aaaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGc                                                                     >  1:447/1‑139 (MQ=255)

                                                      aaaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGc                                                                     <  2:447/139‑1 (MQ=255)

                                                              gCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCTGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcg                                                                                                                          <  2:620791/78‑1 (MQ=255)

                                                              gCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCTGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcg                                                                                                                          >  1:620791/1‑78 (MQ=255)

                                                                 gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc                                                          <  2:739295/139‑1 (MQ=255)

                                                                 gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                         <  2:359066/139‑1 (MQ=255)

                                                                  ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                         <  2:269885/139‑1 (MQ=255)

                                                                  ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                         <  1:793916/139‑1 (MQ=255)

                                                                  ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                         <  2:377309/139‑1 (MQ=255)

                                                                    aTCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAAt                                                       <  2:956176/139‑1 (MQ=255)

                                                                    aTCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAAt                                                       <  2:873953/139‑1 (MQ=255)

                                                                                    aTGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcg                                                                                                                          <  1:78506/56‑1 (MQ=255)

                                                                                    aTGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTgcgcg                                                                                                                          >  2:78506/1‑56 (MQ=255)

                                                                                    aTGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGt                                                                                                  <  1:764721/80‑1 (MQ=255)

                                                                                    aTGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGt                                                                                                  >  2:764721/1‑80 (MQ=255)

                                                                                                aGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAg                           >  2:159183/1‑139 (MQ=255)

                                                                                                aGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAg                           >  2:773587/1‑139 (MQ=255)

                                                                                                 gCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGc                          <  1:773587/139‑1 (MQ=255)

                                                                                                           aTCGTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAg                <  2:56092/139‑1 (MQ=255)

                                                                                                              gTCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTg             >  1:810912/1‑139 (MQ=255)

                                                                                                               tCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGa            >  1:53471/1‑139 (MQ=255)

                                                                                                               tCTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTACTCGTACAACGGATCCCGTATCTCCGGCAATCTGAAGACAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGa            >  1:537502/1‑139 (MQ=255)

                                                                                                                cTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGAt           <  1:220882/139‑1 (MQ=255)

                                                                                                                cTTTAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGAt           >  1:346546/1‑139 (MQ=255)

                                                                                                                 tttAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATc          <  1:148326/139‑1 (MQ=255)

                                                                                                                 tttAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATc          <  1:302540/139‑1 (MQ=255)

                                                                                                                   tAATGTCGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCATTCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCAc        >  1:568475/1‑139 (MQ=255)

                                                                                                                         cGAGGATTTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCAGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTg  >  1:793186/1‑139 (MQ=255)

TTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TTTTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTG  >  NC_000913/2763736‑2763994

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A