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
A13 F121 I0 R1	43	32.8	695000	96.9%	673455	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	638,614	G→T	100%	T14K (ACA→AAA)	thiD ←	phosphomethylpyrimidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	638,614	0	G	T	100.0%	95.1 / NA	32	T14K (ACA→AAA)	thiD	phosphomethylpyrimidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (8/24); total (8/24)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CATCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGA  >  CP000730/638477‑638747

cATCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTttgt                                                                                                                                    <  2:333262/141‑1 (MQ=255)

cATCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTttgt                                                                                                                                    <  1:311731/141‑1 (MQ=255)

    cATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGa                                                                                                                                >  2:156702/1‑141 (MQ=255)

     aTTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGaa                                                                                                                               <  1:270180/141‑1 (MQ=255)

     aTTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGaa                                                                                                                               <  1:37942/141‑1 (MQ=255)

            aTGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACTTGCGCCAGCACTTTTGTCAGAACCGGCaa                                                                                                                        <  1:289243/141‑1 (MQ=255)

                   aaCATCGTGTGACCATGTATTTTTATCCATCGTCACGATGGCAGTTAAAGCGACCATGTCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTTTTaa                                                                                                                 <  1:234496/141‑1 (MQ=255)

                    aCATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTaaa                                                                                                                <  1:198591/141‑1 (MQ=255)

                                   gTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCCTGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCGGCGTCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGcc                                                                                                 <  1:164424/141‑1 (MQ=255)

                                           ttCCATAGTAACGCTAGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGCAACGTTTCCCAATCTGCTTGCATACCTGCGCCAGCACTTTCTTCAGAACCGGCAATTTTTAAAACTTTCTTTAAAGTCATTGAGCt                                                                                         <  2:47932/140‑1 (MQ=255)

                                           aTCCATAGTTACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCt                                                                                         <  2:214195/141‑1 (MQ=255)

                                                          ggCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACataat                                                                          >  1:72025/1‑141 (MQ=255)

                                                               ttACAGCGACCATGCCATACGAATCGAAGTCTTGGAACGTTTGCAAATCTGCTTCCCTACCTGCGCCAGCACTTTTGTCAGCACCTGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAatat                                                                     <  2:208518/141‑1 (MQ=255)

                                                                              cATATGTATCTACTTCTTGGACCGTTTTCAAATCTCCTTGCATACCTGCGCCAGCTCTTTTGTCAGAACCGGCAATTGTAAAAGCTTTCTTTAAAGCCATTGAGCCTCTCTCCTACATAATAATATTGTATTCatcatatc                                                      <  2:206899/141‑1 (MQ=255)

                                                                               aTACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCatcatatca                                                     <  2:341166/141‑1 (MQ=255)

                                                                                  cGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCAttt                                                  >  2:240319/1‑141 (MQ=255)

                                                                                    tATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTTTATTCATCATATCAttttt                                                <  1:224593/141‑1 (MQ=255)

                                                                                       cTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAAc                                             <  1:158221/141‑1 (MQ=255)

                                                                                        tAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAAcc                                            <  1:5103/141‑1 (MQ=255)

                                                                                         acttCTTGGAACGCTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTACAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTGATCATATCATTTTTAACCt                                           <  1:206911/139‑1 (MQ=255)

                                                                                              ttGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTg                                      <  2:304881/141‑1 (MQ=255)

                                                                                                ggAACGTTTTCAACTCTGCTTGCATACCTGCGCCAGCACTTTTGTAAGAACCGGCAATTGTTAAAACTTTCTTTAATGCCATTGAGCTTCACTCATACATAATATTATTGTATTCATCATATCATTTTTAACCTAATTGaa                                    <  2:118720/141‑1 (MQ=255)

                                                                                                ggAACGTTTTCAAATCTGCTTGCATACCTGCACCCGCACTTTTGTAAGGGCGGACTAATGAGAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATAATATCATTTTTAACCTAATTGaa                                    >  2:156440/1‑141 (MQ=255)

                                                                                                ggAACCTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCTGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGaa                                    <  2:63779/141‑1 (MQ=255)

                                                                                                   aCGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTTTATTCCTCATATCATTTTTACCCTAATTGaaaaa                                 >  1:102854/1‑141 (MQ=255)

                                                                                                               ccgtttGCATACCTGTCACAGCAATTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTACAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCAAAAAAAAAAATATTAAGCATTc                     <  2:269006/137‑1 (MQ=255)

                                                                                                                    tGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAatat                >  1:216774/1‑141 (MQ=255)

                                                                                                                     gaaTACCTGCCCCAGCTCTTTTGTCAGCACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATAtt               <  2:128837/139‑1 (MQ=255)

                                                                                                                     gCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATAtt               >  1:136766/1‑141 (MQ=255)

                                                                                                                         aCCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTtgat           <  1:251872/141‑1 (MQ=255)

                                                                                                                           cTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTtgatga         <  1:240319/141‑1 (MQ=255)

                                                                                                                              cgcCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTtgattgttg      >  2:242475/1‑136 (MQ=255)

                                                                                                                                ccAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGAttgtt    <  1:4594/141‑1 (MQ=255)

                                                                                                                                  aGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGa  <  2:47987/141‑1 (MQ=255)

CATCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGA  >  CP000730/638477‑638747

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A