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	1,756,432	T→C	53.8%	N340N (AAT→AAC)	pssA →	phosphatidylserine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,756,432	0	T	C	53.8%	37.2 / 157.9	186	N340N (AAT→AAC)	pssA	phosphatidylserine synthase
Reads supporting (aligned to +/- strand): ref base T (14/72); new base C (28/72); total (42/144)
Fisher's exact test for biased strand distribution p-value = 7.80e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 186 total aligned reads displayed.

TTGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGATGTGG  >  minE/1756370‑1756498

ttGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGAc                                                              <  1:1008322/69‑1 (MQ=255)

ttGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGAc                                                              <  1:2309237/69‑1 (MQ=255)

ttGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGAc                                                              <  1:2692617/69‑1 (MQ=255)

ttGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGAc                                                              <  1:3271593/69‑1 (MQ=255)

ttGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGAc                                                              <  1:388911/69‑1 (MQ=255)

ttGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGAc                                                              <  1:144724/69‑1 (MQ=255)

ttGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGAc                                                              <  1:687378/69‑1 (MQ=255)

ttGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGAc                                                              <  1:524726/69‑1 (MQ=255)

  gCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTGACCa                                                            >  1:359234/1‑69 (MQ=255)

  gCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTGACCa                                                            >  1:2852016/1‑69 (MQ=255)

     ttATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTGACCAGc                                                          <  1:1455917/68‑1 (MQ=255)

               gagaTCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGACCAGTTAGTAGTTCg                                                <  1:976787/68‑1 (MQ=255)

               gagaTCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGACCAGTTAGTAGTTCg                                                <  1:3073973/68‑1 (MQ=255)

               gagaTCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGACCAGTTAGTAGTTCg                                                <  1:1507944/68‑1 (MQ=255)

               gagaTCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGACCAGTTAGTAGTTCg                                                <  1:423666/68‑1 (MQ=255)

               gagaTCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGACCAGTTAGTAGTTCg                                                <  1:420768/68‑1 (MQ=255)

               gagaTCAATCTGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGACCAGTTAGTAGTTCg                                                <  1:2149545/68‑1 (MQ=255)

                        cTGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGATTCGGTTATGGaaa                                      <  1:2520135/69‑1 (MQ=255)

                         tGCGTCGTTTCCTGAGTCGTTTACAGTATTACGTCAACACTGACCAGTTAGTAGTTCg                                                <  1:1399586/58‑1 (MQ=255)

                         tGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTg                                                                <  1:2295622/42‑1 (MQ=255)

                         tGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTg                                                                <  1:2838370/42‑1 (MQ=255)

                         tGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTg                                                                <  1:88015/42‑1 (MQ=255)

                         tGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTg                                                                <  1:1145715/42‑1 (MQ=255)

                         tGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTg                                                                <  1:2210671/42‑1 (MQ=255)

                         tGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTg                                                                <  1:479980/42‑1 (MQ=255)

                               gtTTACTGAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCg                                                >  1:2149458/1‑52 (MQ=255)

                                 ttCCTGAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATgacgac                             <  1:2089991/69‑1 (MQ=255)

                                 ttCCTGAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATgacgac                             <  1:851499/69‑1 (MQ=255)

                                      gAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGacaaca                         <  1:2202632/68‑1 (MQ=255)

                                      gAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGacaaca                         <  1:1249782/68‑1 (MQ=255)

                                      gAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGacaaca                         <  1:1805468/68‑1 (MQ=255)

                                      gAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGacaaca                         <  1:3355795/68‑1 (MQ=255)

                                      gAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGacaaca                         <  1:1152528/68‑1 (MQ=255)

                                      gAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGacaaca                         <  1:450893/68‑1 (MQ=255)

                                      gAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGacaaca                         <  1:589929/68‑1 (MQ=255)

                                           gTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATc                   <  1:3237586/69‑1 (MQ=255)

                                           gTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATc                   <  1:73759/69‑1 (MQ=255)

                                              tacAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:2938663/61‑1 (MQ=255)

                                              tacAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:3010465/61‑1 (MQ=255)

                                              tacAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:2736018/61‑1 (MQ=255)

                                              tacAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:3214553/61‑1 (MQ=255)

                                              tacAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:1011682/61‑1 (MQ=255)

                                              tacAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:1958922/61‑1 (MQ=255)

                                              tacAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:199133/61‑1 (MQ=255)

                                              tacAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:2050686/61‑1 (MQ=255)

                                              tGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCAc                 >  1:637118/1‑68 (MQ=255)

                                              tGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCAc                 >  1:2248073/1‑68 (MQ=255)

                                               acAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCt                      <  1:430604/61‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:2951638/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:2881512/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:1802203/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:155502/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:2649063/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:608397/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:2504962/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:685084/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:2357395/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:938789/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:2328344/68‑1 (MQ=255)

                                                cAGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:2276683/68‑1 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:1130465/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:1595799/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:394084/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:1718658/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:177498/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:3136334/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:1869901/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:2262929/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:2751207/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:246826/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:2609418/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:2386005/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:2657044/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:2712524/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:2916145/1‑55 (MQ=255)

                                                 aGTATTACGTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGacaa                           >  1:2986943/1‑55 (MQ=255)

                                                     ttACGTCAATACTGACCAGCTATTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAgg         <  1:1189713/69‑1 (MQ=255)

                                                     ttACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAgg         <  1:2790983/69‑1 (MQ=255)

                                                     ttACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAgg         <  1:1079087/69‑1 (MQ=255)

                                                     ttACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAgg         <  1:2345761/69‑1 (MQ=255)

                                                       aCGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGa       <  1:2812838/69‑1 (MQ=255)

                                                       aCGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGa       >  1:1568515/1‑69 (MQ=255)

                                                       aCGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGa       <  1:924465/69‑1 (MQ=255)

                                                       aCGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGa       <  1:460740/69‑1 (MQ=255)

                                                       aCGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGa       <  1:147300/69‑1 (MQ=255)

                                                       aCGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGa       <  1:1359223/69‑1 (MQ=255)

                                                         gTCAACACTGACCAGTTAGTAGTTCGGTTATGGAAAGATGACGACAACACCTATCACCt               <  1:1657480/59‑1 (MQ=255)

                                                           cAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGAtgtg   <  1:767440/69‑1 (MQ=255)

                                                           cAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGAtgtg   <  1:1184458/69‑1 (MQ=255)

                                                           cAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGAtgtg   <  1:1897055/69‑1 (MQ=255)

                                                           cAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGAtgtg   <  1:2746133/69‑1 (MQ=255)

                                                           cAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGAtgtg   <  1:3307606/69‑1 (MQ=255)

                                                           cAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGAtgtg   <  1:1928534/69‑1 (MQ=255)

                                                            aaTACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGATGTgg  <  1:1251077/69‑1 (MQ=255)

                                                            aaTACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGATGTgg  <  1:1735889/69‑1 (MQ=255)

                                                            aaTACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGATGTgg  <  1:2354522/69‑1 (MQ=255)

                                                            aaTACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGATGTgg  <  1:943667/69‑1 (MQ=255)

                                                            aaTACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGATGTgg  <  1:1066702/69‑1 (MQ=255)

                                                             aTACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGAtgtg   <  1:1967003/67‑1 (MQ=255)

                                                             aTACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGATGTgg  <  1:1827047/68‑1 (MQ=255)

TTGCCTTATCTCTATGAGATCAATCTGCGTCGTTTCCTGAGCCGTTTGCAGTATTACGTCAATACTGACCAGCTAGTGGTTCGGTTATGGAAAGATGACGACAACACCTATCACCTGAAAGGGATGTGG  >  minE/1756370‑1756498

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