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
A3 F28 I1 R1	124	90.1	3003320	99.2%	2979293	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,163,379	A→G	E40E (GAA→GAG)	thiK →	thiamine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,163,379	0	A	G	100.0%	172.8 / NA	46	E40E (GAA→GAG)	thiK	thiamine kinase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (0/46); total (0/46)

TATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCG  >  NC_000913/1163243‑1163510

tATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCAt                                                                                                                                  <  2:993679/140‑1 (MQ=255)

      gTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGc                                                                                                                            <  1:1061641/140‑1 (MQ=255)

        cAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCa                                                                                                                          <  2:8079/140‑1 (MQ=255)

             aaaGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGtt                                                                                                                     <  1:779137/140‑1 (MQ=255)

              aaGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGGTTTCTCATTGTGCATCAGGGCCAGCGctt                                                                                                                    >  1:385021/1‑140 (MQ=255)

                 gTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTttgt                                                                                                                 <  1:1261091/140‑1 (MQ=255)

                     cGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCCTTTTGCCTCAGGGCCCGCGGTTTGTtttg                                                                                                             >  2:413585/1‑140 (MQ=255)

                     cGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCCTTTAGCATCAGGGGCAGCGTTTTGTtgtg                                                                                                             >  1:164322/1‑140 (MQ=255)

                     cGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGGTTTTTCCTTTTGCATCAAGGGCCGCGTTTttttgtt                                                                                                             >  1:1366425/1‑139 (MQ=255)

                       tttCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTGGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGACAGCGTTTTGTTGTGCg                                                                                                           <  2:315963/140‑1 (MQ=255)

                        ttCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGt                                                                                                          <  1:229599/140‑1 (MQ=255)

                         tCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTc                                                                                                         <  2:573929/140‑1 (MQ=255)

                          cGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCCTTTTGCATCAGGGGCCGCGGTTTTTtttgtggcg                                                                                                        >  2:560386/1‑135 (MQ=255)

                           gcagcaATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAg                                                                                                       <  1:1251181/140‑1 (MQ=255)

                           gcagcaATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAg                                                                                                       <  1:233512/140‑1 (MQ=255)

                            cagcaATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCTTTTTGGATCAAGGCCACCGCTTTTTTGTTCGTCGGc                                                                                                      >  1:916412/1‑140 (MQ=255)

                             agcaATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGcc                                                                                                     <  2:722987/140‑1 (MQ=255)

                                aataatCCCGTCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGATTTCTCATTGTGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  2:1127689/140‑1 (MQ=255)

                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  2:616553/140‑1 (MQ=255)

                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  2:170023/140‑1 (MQ=255)

                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  2:1272040/140‑1 (MQ=255)

                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  1:1008878/140‑1 (MQ=255)

                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  1:457892/140‑1 (MQ=255)

                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  1:17743/140‑1 (MQ=255)

                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  1:313483/140‑1 (MQ=255)

                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                  <  1:504896/140‑1 (MQ=255)

                                  taatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGGTTTTTTTTTTTGCAACAGGGGCAGCGGTTTTTTTTTGGTCGGCCGcccc                                                                                                >  1:1134789/1‑137 (MQ=255)

                                          tCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGAt                                                                                        <  1:681435/140‑1 (MQ=255)

                                                gcgACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGcgccg                                                                                  <  1:552784/140‑1 (MQ=255)

                                                gcgACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGcgccg                                                                                  <  1:1295708/140‑1 (MQ=255)

                                                 cgacgaATTGCTGTCGCGCTTTTTCCCGCAGTATCGTCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGcgccgc                                                                                 <  2:640171/140‑1 (MQ=255)

                                                        ttGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCcgc                                                                          <  1:628689/140‑1 (MQ=255)

                                                             gTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCTTTTTGCATCAGGGCCCACGGTTTGTTGTGGGTCAGCCCCACCAGCCTGATGCGCCCCAGGCCCCGTTCt                                                                     >  2:928057/1‑140 (MQ=255)

                                                             gTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCt                                                                     <  2:951924/140‑1 (MQ=255)

                                                                          ccGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCg                                                        <  1:1302887/140‑1 (MQ=255)

                                                                             cAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGTAGTCCGCGTTCTTGCGCCAGTATCGGGc                                                     <  2:203559/140‑1 (MQ=255)

                                                                             cAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGc                                                     <  2:939328/140‑1 (MQ=255)

                                                                              aGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCt                                                    <  1:470762/140‑1 (MQ=255)

                                                                                     tcCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATcac                                             <  2:164322/140‑1 (MQ=255)

                                                                                        cGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAAc                                          <  1:448064/140‑1 (MQ=255)

                                                                                          tCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTa                                        <  2:1366425/140‑1 (MQ=255)

                                                                                          tCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTa                                        <  2:362009/140‑1 (MQ=255)

                                                                                               acgTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgc                                   <  2:250023/140‑1 (MQ=255)

                                                                                               acgTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgc                                   <  1:198024/140‑1 (MQ=255)

                                                                                               acgTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgc                                   <  1:524033/140‑1 (MQ=255)

                                                                                               acgTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCACACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgc                                   <  1:928057/140‑1 (MQ=255)

                                                                                                         gTGGGCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCa                         <  1:256188/140‑1 (MQ=255)

                                                                                                            ggCTTAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCg                      <  2:766530/140‑1 (MQ=255)

                                                                                                               ttAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAg                   <  1:1199255/140‑1 (MQ=255)

                                                                                                                tAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGc                  <  1:953539/140‑1 (MQ=255)

                                                                                                                tAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGc                  <  2:1134789/140‑1 (MQ=255)

                                                                                                                tAGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCCTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGc                  <  2:782690/140‑1 (MQ=255)

                                                                                                                 aGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGcc                 <  1:50724/140‑1 (MQ=255)

                                                                                                                 aGTGGCGGGAGTTTTCTCATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCACACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGcc                 <  1:1155622/140‑1 (MQ=255)

                                                                                                                                ctcATTGAGCATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCg  <  1:1441321/140‑1 (MQ=255)

TATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCG  >  NC_000913/1163243‑1163510

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A