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
A15 F177 I1 R2	35	38.3	831348	95.5%	793937	139.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	638,614	G→T	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%	119.3 / NA	35	T14K (ACA→AAA)	thiD	phosphomethylpyrimidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (24/11); total (24/11)

CATCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGAAA  >  CP000730/638477‑638749

cATCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTttgt                                                                                                                                      >  2:31388/1‑141 (MQ=255)

      ttGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAAc                                                                                                                                >  2:292414/1‑141 (MQ=255)

        ggTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCg                                                                                                                              >  2:403040/1‑141 (MQ=255)

          tAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGc                                                                                                                            <  1:320636/141‑1 (MQ=255)

           aaTGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCa                                                                                                                           >  1:82020/1‑141 (MQ=255)

                  tAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTa                                                                                                                    >  1:52536/1‑141 (MQ=255)

                  tAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTa                                                                                                                    >  2:268627/1‑141 (MQ=255)

                   aaCATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTaa                                                                                                                   >  1:360743/1‑141 (MQ=255)

                    aCATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTaaa                                                                                                                  >  2:286568/1‑141 (MQ=255)

                      aTCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAAc                                                                                                                >  1:268052/1‑141 (MQ=255)

                        cGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAActt                                                                                                              >  2:141871/1‑141 (MQ=255)

                                      tCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCTAGCACTTTTGTCAGAGCCGGCAATTGTTAAAACTTTCTTTAAAGCCAtt                                                                                                <  1:110458/141‑1 (MQ=255)

                                                   tAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCt                                                                                   <  1:362548/141‑1 (MQ=255)

                                                      cGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACa                                                                                >  1:238545/1‑141 (MQ=255)

                                                               ttAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAatat                                                                       <  1:257036/141‑1 (MQ=255)

                                                               ttAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAatat                                                                       <  1:156141/141‑1 (MQ=255)

                                                                  aaGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGt                                                                    >  2:40686/1‑141 (MQ=255)

                                                                      gACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCTATTGTTAAAACTTTCTTTAAAGCCATTTAGCTTCACTCCTACATAATAATATTGTATtc                                                                >  2:272383/1‑141 (MQ=255)

                                                                      gACCATGCCATACGTATCTAATCCTTGGAACGTTTTCAAATCTGCTTGAACACCTTCGCCAGCTCCTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTAttt                                                                >  1:301660/1‑140 (MQ=255)

                                                                      gACCATGAAATACGTATCTAATTCTTGCAACGTTTTCAAATCTGCTGGCATCCCTGCGCCAGGACTTTTGTCAAAACTGGCAACGGTTAAGGCTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTAtta                                                                >  2:322423/1‑140 (MQ=255)

                                                                          aTGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATttatca                                                            >  1:120955/1‑141 (MQ=255)

                                                                           tGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTcatcat                                                           >  2:159459/1‑141 (MQ=255)

                                                                             ccATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCatcatat                                                         <  2:137479/141‑1 (MQ=255)

                                                                                        tAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAAcc                                              <  2:264609/141‑1 (MQ=255)

                                                                                            tCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAAt                                          >  2:354154/1‑141 (MQ=255)

                                                                                                  aaCGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGaaaa                                    >  1:147584/1‑141 (MQ=255)

                                                                                                         tCAAATCTGCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTaa                             >  2:266889/1‑141 (MQ=255)

                                                                                                                 gCTTGCATACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATTTTGTATTCATCATATCATTTTTAACCTAATTGAAAAGTATTAAGCATTTaa                     >  2:100510/1‑141 (MQ=255)

                                                                                                                       aTACCTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTtg               <  2:268052/141‑1 (MQ=255)

                                                                                                                          ccTGCGCCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTtgatg            >  1:28356/1‑141 (MQ=255)

                                                                                                                            tGCGCCAGCACTTTTGTCAGCACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTgatgat          >  1:218728/1‑141 (MQ=255)

                                                                                                                             gcgcCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCAt                                                                                                 >  1:243970/1‑53 (MQ=255)

                                                                                                                             gcgcCAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCAt                                                                                                 <  2:243970/53‑1 (MQ=255)

                                                                                                                                ccAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGAttgtt      <  2:388432/141‑1 (MQ=255)

                                                                                                                                ccAGCACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGAttgtt      <  1:348375/141‑1 (MQ=255)

                                                                                                                                    cACTTTTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGaaa  >  1:58826/1‑141 (MQ=255)

CATCCATTGGTAATGGTGTAACATCGTGTGACCATGTATCTTTATCCATAGTAACGATGGCAGTTAAAGCGACCATGCCATACGTATCTAATTCTTGGAACGTTTTCAAATCTGCTTGCATACCTGCGCCAGCACTTGTGTCAGAACCGGCAATTGTTAAAACTTTCTTTAAAGCCATTGAGCTTCACTCCTACATAATAATATTGTATTCATCATATCATTTTTAACCTAATTGAAAAATATTAAGCATTCAATATTTGATGATTGTTGAAA  >  CP000730/638477‑638749

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

GATK/CNVnator alignment

N/A