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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,194,755	C→T	E449K (GAG→AAG)	thiC ←	phosphomethylpyrimidine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,194,755	0	C	T	96.7%	105.3 / ‑3.6	30	E449K (GAG→AAG)	thiC	phosphomethylpyrimidine synthase
Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (13/16); total (14/16)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.95e-01

ACGTAACAGAGCATCGCGCAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTCGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTGGTCAGTTCGCCCAGCGTATGCAGCTCGGCAAACTGCGCTTCATCGTTGGCGTCC  >  NC_000913/4194613‑4194894

aCGTAACAGAGCATCGCGCAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCata                                                                                                                                      <  1:121122/150‑1 (MQ=255)

     aCAGAGCATCGCGCAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTgcgg                                                                                                                                >  2:606157/1‑151 (MQ=255)

     aCAGAGCATCGCGCAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTgcgg                                                                                                                                >  2:544931/1‑151 (MQ=255)

       agagCATCGCGCAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTgcggcg                                                                                                                              <  1:205074/151‑1 (MQ=255)

              cgcgCAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGatcat                                                                                                                        <  1:553917/150‑1 (MQ=255)

                 gcAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTg                                                                                                                     <  2:194419/150‑1 (MQ=255)

                 gcAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGc                                                                                                                    >  2:630521/1‑151 (MQ=255)

                           cAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGt                                                                                                          >  2:510314/1‑151 (MQ=255)

                            aGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTg                                                                                                         <  2:126274/151‑1 (MQ=255)

                                      cgccgcACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCt                                                                                               >  1:200692/1‑151 (MQ=255)

                                      cgccgcACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTCGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCt                                                                                               >  2:241239/1‑151 (MQ=255)

                                       gccgcACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCtt                                                                                              <  1:566683/151‑1 (MQ=255)

                                       gccgcACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCtt                                                                                              <  2:335857/151‑1 (MQ=255)

                                          gcACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCaa                                                                                           <  1:5842/151‑1 (MQ=255)

                                                           gAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTc                                                                           >  1:203777/1‑150 (MQ=255)

                                                            aaGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCat                                                                         >  2:253267/1‑151 (MQ=255)

                                                            aaGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCat                                                                         >  2:451815/1‑151 (MQ=255)

                                                               tGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATAtt                                                                      >  2:192108/1‑151 (MQ=255)

                                                                ggTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATAtt                                                                      <  2:14364/150‑1 (MQ=255)

                                                                   cATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCa                                                                  <  2:492070/151‑1 (MQ=255)

                                                                         ccGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAAt                                                            >  2:174338/1‑151 (MQ=255)

                                                                         ccGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAAt                                                            <  1:30553/151‑1 (MQ=255)

                                                                              gcAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGGCATATTCCCAGGCAATTTTgg                                                       >  2:226755/1‑151 (MQ=255)

                                                                               cAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTgg                                                       <  2:551322/150‑1 (MQ=255)

                                                                                aaTATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTGGt                                                      <  2:341138/150‑1 (MQ=255)

                                                                                          gTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTGGTCAGTTCGCCCa                                           <  1:83128/151‑1 (MQ=255)

                                                                                                  ccccAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTCGTCAGTTCGCCCAGCGTATg                                    >  2:188985/1‑150 (MQ=255)

                                                                                                                           tGGCAGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTAGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTGGTCAGTTCGCCCAGCGTATGCAGCTCGGCAAACTGCGCTTCATCGt          >  2:249324/1‑151 (MQ=255)

                                                                                                                               aGTGCTCTAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTGGTCAGTTCGCCCAGCGTATGCAGCTCGGCAAACTGCGCTTCATCGTTGGc      <  1:483418/151‑1 (MQ=255)

                                                                                                                                     ctAACTCCTTGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTGGTCAGTTCGCCCAGCGTATGCAGCTCGGCAAACTGCGCTTCATCGTTGGCGTcc  <  2:482384/149‑1 (MQ=255)

ACGTAACAGAGCATCGCGCAGCCAAACCAGCCAATCATCGCCGCACCAATCCCCGACGTGAAGTGGTCATAGCCCGGCGCAATATCGGTAGTTAGCGGCCCCAGAGTGTAAAACGGCGCTTCGTGGCAGTGCTCTAACTCCTCGGTCATATTGCGGCGGATCATCTGCATCGGCACGTGGCCTGGGCCTTCAATCATCACCTGCACGTCATATTCCCAGGCAATTTTGGTCAGTTCGCCCAGCGTATGCAGCTCGGCAAACTGCGCTTCATCGTTGGCGTCC  >  NC_000913/4194613‑4194894

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A