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 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,886,479	G→A	42.8%	T647T (ACG→ACA)	barA →	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,886,479	0	G	A	42.8%	25.0 / 56.5	77	T647T (ACG→ACA)	barA	hybrid sensory histidine kinase, in two‑component regulatory system with UvrY
Reads supporting (aligned to +/- strand): ref base G (17/27); new base A (10/23); total (27/50)
Fisher's exact test for biased strand distribution p-value = 4.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.70e-01

GGTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGT  >  minE/1886420‑1886547

ggTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:1016376/69‑1 (MQ=255)

ggTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:2967943/69‑1 (MQ=255)

ggTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:3144744/69‑1 (MQ=255)

ggTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:3249181/69‑1 (MQ=255)

ggTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:1986022/69‑1 (MQ=255)

ggTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:1903604/69‑1 (MQ=255)

 gTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:3312959/68‑1 (MQ=255)

 gTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:1386143/68‑1 (MQ=255)

   aTCGGCGCGTGTCTGCTGAAACCATTAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGtcat                                                          <  1:1075248/69‑1 (MQ=255)

   aTCGGCGCGTGTCTGCTGAAACCATTAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGtcat                                                          <  1:239624/69‑1 (MQ=255)

   aTCGGCGCGTGTCTGCTGAAACCATTAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGtcat                                                          <  1:3096685/69‑1 (MQ=255)

   aTCGGCGCGTGTCTGCTGAAACCATTAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGtcat                                                          <  1:3124107/69‑1 (MQ=255)

   aTCGGCGCGTGTCTGCTGAAACCATTAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGtcat                                                          <  1:867339/69‑1 (MQ=255)

   aTCGGCGCGTGTCTGCTGAAACCATTAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGtcat                                                          <  1:775360/69‑1 (MQ=255)

         gcgTGTCTGCTGAAACCATTAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGtcat                                                          <  1:1958330/63‑1 (MQ=255)

               ctgctgAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGt                                                             <  1:37205/54‑1 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         <  1:2947058/69‑1 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         <  1:317822/69‑1 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         <  1:3176316/69‑1 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         <  1:2008658/69‑1 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         <  1:1045466/69‑1 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         >  1:10171/1‑69 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         <  1:2212349/69‑1 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         >  1:2258933/1‑69 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         <  1:1187058/69‑1 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         >  1:2416872/1‑69 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         >  1:161824/1‑69 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         >  1:1581125/1‑69 (MQ=255)

                    gAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCt                                         <  1:2538935/69‑1 (MQ=255)

                        ccATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTg                                     <  1:1982318/69‑1 (MQ=255)

                        ccATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTg                                     <  1:2551079/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:602692/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:1240590/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:2863490/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:1280492/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:2531791/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:10044/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:1065199/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:3284754/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:745618/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:922288/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:1895612/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:337763/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:352694/69‑1 (MQ=255)

                           ttAACACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTATTGCCt                                  <  1:440434/69‑1 (MQ=255)

                           ttAAAACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:689859/69‑1 (MQ=255)

                             aaCACGTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:2898071/1‑39 (MQ=37)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:2561926/1‑39 (MQ=38)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:512951/1‑39 (MQ=38)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:266751/1‑39 (MQ=38)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:357094/1‑39 (MQ=38)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:997750/1‑39 (MQ=38)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:3280675/1‑39 (MQ=38)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:1360380/1‑39 (MQ=38)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:202002/1‑39 (MQ=38)

                             aaCACCTACGCGCCTGTTGCCTGCCCTGACAGAATTTTg                                                              >  1:2016002/1‑39 (MQ=38)

                              acacCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTg                                     <  1:1061388/63‑1 (MQ=255)

                                 ccTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAAcc                            <  1:1955496/69‑1 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:722600/1‑50 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:133643/1‑50 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:2229162/1‑50 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:884061/1‑50 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:3140972/1‑50 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:2181997/1‑50 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:826598/1‑50 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:1299557/1‑50 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTa                               <  1:483617/64‑1 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTa                               <  1:660037/64‑1 (MQ=255)

                                   tACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTa                               <  1:2552570/64‑1 (MQ=255)

                                   tACACGACTGTTGCCTGCCCTGACGGAATTTTGTCATCACaaacaaaaca                                             >  1:439474/1‑50 (MQ=255)

                                    acgcGCCTGTTGCCTGCCCTGACAGAATTTTGTCATCACAAACAAAACACGCTTTTGCCt                                  <  1:1625896/57‑1 (MQ=255)

                                     cacGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGAt                         >  1:2209107/1‑68 (MQ=255)

                                     cacGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGAt                         >  1:2383965/1‑68 (MQ=255)

                                     cacGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGAt                         >  1:2488722/1‑68 (MQ=255)

                                       cGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGaa                      <  1:2073402/69‑1 (MQ=255)

                                       cGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGaa                      <  1:1688121/69‑1 (MQ=255)

                                       cGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGaa                      <  1:645577/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:1353374/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:952056/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:1389750/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:1449811/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:103955/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:488325/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:470017/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:359939/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:1680614/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:3385978/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:1864314/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:1918686/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:3285773/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:1973493/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:3236339/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:2223924/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:2419489/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:2895754/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGt  <  1:2441524/69‑1 (MQ=255)

                                                           ggAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGAAAGt  <  1:1656325/69‑1 (MQ=255)

GGTATCGGCGCGTGTCTGCTGAAACCATTAACACCTACACGCCTGTTGCCTGCCCTGACGGAATTTTGTCATCACAAACAAAACACGCTTTTGCCTGTAACCGATGAAAGTAAGCTGGCAATGACAGT  >  minE/1886420‑1886547

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A