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 F56 I20 R2	1958	92.1	3575798	91.1%	3257551	126.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	2,198,012	G→T	G42G (GGC→GGA)	U712_11010 ←	Chorismate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,198,012	0	G	T	92.9%	95.6 / ‑5.9	42	G42G (GGC→GGA)	U712_11010	Chorismate synthase
Reads supporting (aligned to +/- strand): ref base G (2/1); new base T (1/38); total (3/39)
Fisher's exact test for biased strand distribution p-value = 1.03e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCCAATGCTTCCAATCGTTATTTTCAACGACGAGAGCAATTGGTGAACCGAGTGTTCGTGCATGACGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GGCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGCACACCTTCAATAATGGTTGTCAGTTGGGGGCCGTGTGATTCTCCGGCTGTTAAATATCTCATGACTTCTT  >  CP006881/2197885‑2198145

tCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGTGGGCGTTTTTggg                                                                                                                             >  8:309277/1‑138 (MQ=255)

  cAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGt                                                                                                                           <  7:75501/138‑1 (MQ=255)

       cTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGc                                                                                                                      <  3:5828/138‑1 (MQ=255)

          ccAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GGGCGTTTTTGGGTCTgggcg                                                                                                                    >  6:177948/1‑134 (MQ=255)

             aTCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCa                                                                                                               <  3:168391/139‑1 (MQ=255)

                   aTTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTg                                                                                                         <  3:251976/139‑1 (MQ=255)

                    ttttCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGGCTTTATCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGGCTGGCAAGCTCAAAATTg                                                                                                         <  8:60014/138‑1 (MQ=255)

                          actacgaGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCtt                                                                                                  <  1:76207/136‑1 (MQ=255)

                           ctacgaGAGCAATTGGCGAACCTAGTGTCCGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCCTGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTtc                                                                                                 <  8:322929/137‑1 (MQ=255)

                           ctacgaGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTGTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTAGTTTTTGGAGTCTGGCAAGCTCAAAATTGATATCTtc                                                                                                 <  1:295233/137‑1 (MQ=255)

                           ctacgaGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTtc                                                                                                 <  5:314458/137‑1 (MQ=255)

                                agagCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCg                                                                                            <  8:423394/139‑1 (MQ=255)

                                agagCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCg                                                                                            <  4:400046/139‑1 (MQ=255)

                                      aTTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGt                                                                                      <  3:276453/139‑1 (MQ=255)

                                       ttGGCGAACCGCGTGTACGTGACTGGCGCACCCCGCTCATAATTTTTGCCTGGTCTTTTTCTATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGTCGTCTGGGAAGCTCAAAATTGATATCTTCCTCCGTTATGTa                                                                                     <  6:436314/139‑1 (MQ=255)

                                           cgAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGTTCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGc                                                                                 <  2:82333/138‑1 (MQ=255)

                                           cgAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGc                                                                                 <  4:284585/138‑1 (MQ=255)

                                               ccGAGTGTACGTGCATGGCGCACCCCGCTCATAATTATGGCCTGGGCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCgg                                                                             <  8:204382/139‑1 (MQ=255)

                                               ccGAGTGGACGTGCATGGCTCAGCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCgg                                                                             <  6:71953/139‑1 (MQ=255)

                                                  aGTGTACGTGCATGGCGCACCCCGCGCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCTGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCggcag                                                                          >  7:62843/1‑139 (MQ=255)

                                                        cGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCTTGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTATAGCCCGGCAGGtaca                                                                     <  3:77790/138‑1 (MQ=255)

                                                         gTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCTGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACAcc                                                                   <  8:62843/139‑1 (MQ=255)

                                                         gTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACAcc                                                                   <  7:399963/139‑1 (MQ=255)

                                                         gTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACAcc                                                                   <  7:309277/139‑1 (MQ=255)

                                                         gTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACAcc                                                                   <  5:177948/139‑1 (MQ=255)

                                                         gTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACAcc                                                                   <  4:26423/139‑1 (MQ=255)

                                                         gTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACAcc                                                                   <  4:43522/139‑1 (MQ=255)

                                                         gTGCATGGCGCACCCCGCTCATAATTTTGGCCAGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACAcc                                                                   <  5:79071/139‑1 (MQ=255)

                                                         aggCATGGCGCACCCCGCTCTTAATTTTGGCCTGGTCTTTTTCGATGTGCTTGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACAcc                                                                   <  1:405834/137‑1 (MQ=255)

                                                                       ccGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTg                                                     <  3:35275/139‑1 (MQ=255)

                                                                        cGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGt                                                    <  1:207619/139‑1 (MQ=255)

                                                                        cGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGt                                                    <  7:301247/139‑1 (MQ=255)

                                                                        cGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGt                                                    <  5:387914/139‑1 (MQ=255)

                                                                                aTTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGTCAGTTgg                                             <  7:239831/138‑1 (MQ=255)

                                                                                   ttGGCCTGGTCTTTTTCGATCTGCCTGCGGCGGCCGCGGCCGT‑GGCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCATCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGTCAGTTggggg                                          <  2:147105/138‑1 (MQ=255)

                                                                                                   cGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGTCAGTTGGGGGCCGTGTGATTCTCCgg                          <  1:127216/138‑1 (MQ=255)

                                                                                                   cGATCTGCATGCGGCAGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGTCAGTTGGGGGCCGTGTGATTCTCCgg                          <  5:121913/138‑1 (MQ=255)

                                                                                                                  ggccgcggccgT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGTCAGTTGGGGGCCGTGTGATTCTCCGGCTGTTAAATATCTCAt          <  6:419096/139‑1 (MQ=255)

                                                                                                                    ccgcggccgT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGTCAGTTGGGGGCCGTGTGATTCTCCGGCTGTTAAATATCTCATGa        <  4:278188/139‑1 (MQ=255)

                                                                                                                    ccgcggccgT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGTCAGTTGGGGGCCGTGTGATTCTCCGGCTGTTAAATATCTCATGa        <  3:223792/139‑1 (MQ=255)

                                                                                                                    ccgcggccgT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGTACACCCTCAATAATGGTTGTCAGTTGGGGGCCGTGTGATTCTCCGGCTGTTAAATATCTCATGa        <  1:49567/139‑1 (MQ=255)

                                                                                                                          ccgT‑GTCCTTTTCGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTTTGTAAAGCGCGGCTGGTACACCCTCAATAATGGATGTCAGTAGGGGGCCGTGTTATTCTCCGGCTGTTTAATCTCTCATGActtctt  <  7:206304/139‑1 (MQ=255)

TCCAATGCTTCCAATCGTTATTTTCAACGACGAGAGCAATTGGTGAACCGAGTGTTCGTGCATGACGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GGCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTAAAGCCCGGCAGGCACACCTTCAATAATGGTTGTCAGTTGGGGGCCGTGTGATTCTCCGGCTGTTAAATATCTCATGACTTCTT  >  CP006881/2197885‑2198145

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A