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
A17 F172 I0 R1	42	33.2	716278	96.8%	693357	139.9

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%	108.8 / ‑6.5	39	T14K (ACA→AAA)	thiD	phosphomethylpyrimidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/1); new base T (10/28); total (10/29)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGAA  >  CP000730/638479‑638748

tCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTc                                                                                                                                    <  2:318705/140‑1 (MQ=255)

   aTTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGGAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGa                                                                                                                                 <  2:18078/140‑1 (MQ=255)

    ttGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGTACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGaa                                                                                                                                <  2:228681/140‑1 (MQ=255)

    ttGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGaa                                                                                                                                <  1:91735/140‑1 (MQ=255)

       gTAATGGTGTAACAGCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCg                                                                                                                             <  2:302613/140‑1 (MQ=255)

              gatAACATCGTGTAAACATGTATCTTTATCCATAGAAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTg                                                                                                                      <  1:163417/138‑1 (MQ=255)

                tAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGtt                                                                                                                    <  1:177081/140‑1 (MQ=255)

                 aaCATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCGGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTGAAAACTGCTTGCATACCTTCGACAGACCCTTTGTCACAAACAGCAAtttgta                                                                                                                   >  2:88452/1‑136 (MQ=255)

                   cATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTaaa                                                                                                                 >  2:85931/1‑140 (MQ=255)

                      cGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAAct                                                                                                              <  1:96989/140‑1 (MQ=255)

                                         aTCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGc                                                                                           <  1:55251/140‑1 (MQ=255)

                                           ccATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCtt                                                                                         <  1:326335/140‑1 (MQ=255)

                                             aTAGTATCGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCa                                                                                       <  2:178056/140‑1 (MQ=255)

                                                   aCGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTa                                                                                 >  1:342652/1‑140 (MQ=255)

                                                   aCGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGCCCCAACCCGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTa                                                                                 <  1:336090/140‑1 (MQ=255)

                                                   aCGATGGCAGTTAAAGCGAACATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCCTACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAATCCATTGAGCTACACTcaca                                                                                 >  1:85909/1‑137 (MQ=255)

                                                             ttAAAGCGACCATGCCATCCGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACataataata                                                                       >  1:354482/1‑140 (MQ=255)

                                                              tAAAGCGACCATGCCATAAGTATCTCATTCTTGCAACGTTTTCCAATCTGCCTGCATACCTGAGACCGAGTTTGTCTCCGACCAGGTTATGGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAatat                                                                      <  1:352120/140‑1 (MQ=255)

                                                               aacgCGACCATGTCATACGGATCTAATGCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCGAGCACTTTTGTCATAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATGATAtt                                                                     <  2:245752/137‑1 (MQ=255)

                                                               aaaGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATAtt                                                                     <  1:342733/140‑1 (MQ=255)

                                                                  gCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCGGCTTGCATACCTGCGCCAGCACTTTTGTTAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTa                                                                  <  2:10394/140‑1 (MQ=255)

                                                                      ccATGCCATACGTATCAAATTATTGGGACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCACTTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATtca                                                              >  1:183259/1‑140 (MQ=255)

                                                                         tGCCATACGTATCTAATTGTGGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCGATTGTTACATCTTTCTTTAACGCCATTGAGCTTCACTCCTACATAATAATATTGTATtcatcg                                                           >  2:3350/1‑139 (MQ=255)

                                                                          gCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTcatcat                                                          >  2:226004/1‑140 (MQ=255)

                                                                           ccATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCatcata                                                         <  1:19107/140‑1 (MQ=255)

                                                                                 gTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCAttt                                                   <  2:335530/140‑1 (MQ=255)

                                                                                  tATCTACTTCCTGTAACGTTTTAAAATCTGCTTGCATATCTGCGCCAGCACTTTTGTCACAGCCGGCAATTGTTAAAACTTTCTATAAAGCCACTGAGCTTCCATCCTACATAATAATATTGTATTCATCATATCAtttt                                                  <  2:22514/140‑1 (MQ=255)

                                                                                          tCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTaa                                          <  1:102193/140‑1 (MQ=255)

                                                                                           cTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAAt                                         <  2:102319/140‑1 (MQ=255)

                                                                                           cTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAAt                                         <  2:102220/140‑1 (MQ=255)

                                                                                            ttggaattgtttCAAAGCGGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAAtt                                        <  2:72005/131‑1 (MQ=255)

                                                                                            ttGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAAtt                                        <  1:313628/140‑1 (MQ=255)

                                                                                               gAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCTCTCCTAAAGAATAATATTGTATTCATCATATCATTTTTAACCTAATTGaa                                     <  1:336191/140‑1 (MQ=255)

                                                                                                aaCGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGaaa                                    >  1:265395/1‑140 (MQ=255)

                                                                                                  cGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGaaaaa                                  <  2:350672/140‑1 (MQ=255)

                                                                                                    ttttCCAATCCGGTTGCATACCTGCGCCAGCATTTTTGTCAGAACTGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAata                                <  1:62709/140‑1 (MQ=255)

                                                                                                        caaagtttgttGCATTCCTGTGTCAGGACTTTTGGCAGATACGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCATTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAACTATTaa                            <  2:309118/131‑1 (MQ=255)

                                                                                                               gCTTGCAGACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCa                     <  1:15297/140‑1 (MQ=255)

                                                                                                                                  cACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTAATGATTGTTGaa  >  2:283907/1‑140 (MQ=255)

TCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGAA  >  CP000730/638479‑638748

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A