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	1,513,033	C→A	37.5%	intergenic (+156/+276)	pta → / ← ubiX	phosphate acetyltransferase/3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,513,033	0	C	A	37.5%	147.3 / 124.1	160	intergenic (+156/+276)	pta/ubiX	phosphate acetyltransferase/3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase
Reads supporting (aligned to +/- strand): ref base C (63/36); new base A (30/30); total (93/67)
Fisher's exact test for biased strand distribution p-value = 9.95e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 160 total aligned reads displayed.

CTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTTGTGTGTT  >  minE/1512969‑1513097

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:2290444/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:302034/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:202942/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:1530414/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:1517382/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:2581235/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:2395996/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:2387157/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:1047150/67‑1 (MQ=255)

     tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGAGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:2757020/67‑1 (MQ=255)

      gATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:3013369/66‑1 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTTTTAc                                                      >  1:1048420/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa                                                       <  1:2705183/67‑1 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa                                                       >  1:3410456/1‑67 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa                                                       <  1:914382/67‑1 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa                                                       <  1:2626958/67‑1 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa                                                       <  1:3130644/67‑1 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa                                                       <  1:1788900/67‑1 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:2636093/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:810913/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:1756174/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:2654412/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:841704/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:3086888/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:1624534/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:627340/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:3332475/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:336114/1‑68 (MQ=255)

         tATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTAc                                                      >  1:2406208/1‑68 (MQ=255)

             ttGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAAc                                                 >  1:1008315/1‑69 (MQ=255)

               gCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa                                                       <  1:1206679/61‑1 (MQ=255)

                   aaCTGCGCTGCATCAATTAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:162431/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:71785/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:291731/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:3239928/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:35111/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:437654/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:522839/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:559559/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:779170/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:2219959/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:1872379/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:2108914/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:1838865/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:1914383/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:1086135/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:2069284/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:1474083/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:1633567/1‑54 (MQ=255)

                   aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACTTTg                                                          >  1:1090503/1‑54 (MQ=255)

                          cTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:540801/46‑1 (MQ=255)

                                 aaTGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:2421466/39‑1 (MQ=255)

                                  aTGAATTGCGCCATCTCACTTTGCATACTTACCACttt                                                           <  1:2268056/38‑1 (MQ=255)

                                     aaTTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATa                                                   >  1:2709683/1‑43 (MQ=255)

                                     aaTTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATa                                                   >  1:1767848/1‑43 (MQ=255)

                                     aaTTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATa                                                   >  1:1065590/1‑43 (MQ=255)

                                     aaTTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATa                                                   >  1:2346836/1‑43 (MQ=255)

                                       ttGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCttttt                           >  1:3193271/1‑65 (MQ=255)

                                       ttGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCttttt                           >  1:3428733/1‑65 (MQ=255)

                                       ttGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCttttt                           >  1:2663256/1‑65 (MQ=255)

                                       ttGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCttttt                           >  1:1965833/1‑65 (MQ=255)

                                       ttGCGCCATCTCACTTTGCATACTTCCCACTATGTTACATAACCCTCAAGTGAAAATGGCttttt                           >  1:626269/1‑65 (MQ=255)

                                                 tcACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGaa                                      <  1:2840332/44‑1 (MQ=255)

                                                 tcACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGaa                                      <  1:1597925/44‑1 (MQ=255)

                                                 tcACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttg             >  1:2721689/1‑69 (MQ=255)

                                                 tcACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttg             >  1:3380460/1‑69 (MQ=255)

                                                 tcACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttg             >  1:2055807/1‑69 (MQ=255)

                                                 tcACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttg             >  1:719566/1‑69 (MQ=255)

                                                 tcACTTTGCATACCTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttg             >  1:2181786/1‑69 (MQ=255)

                                                       tGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttgtgttgt       >  1:2941455/1‑69 (MQ=255)

                                                       tGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttgtgttgt       >  1:11881/1‑69 (MQ=255)

                                                       tGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttgtgttgt       >  1:1314985/1‑69 (MQ=255)

                                                       tGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttgtgttgt       >  1:935319/1‑69 (MQ=255)

                                                       tGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttgtgttgt       >  1:1578500/1‑69 (MQ=255)

                                                       tGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttgtgttgt       >  1:2032317/1‑69 (MQ=255)

                                                       tGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttgtgttgt       >  1:768018/1‑69 (MQ=255)

                                                           tACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTtgtgtg    <  1:3171116/68‑1 (MQ=255)

                                                           tACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTtgtgtg    <  1:3070361/68‑1 (MQ=255)

                                                           tACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTtgtgtg    <  1:835905/68‑1 (MQ=255)

                                                           tACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTtgtgtg    <  1:2217152/68‑1 (MQ=255)

                                                           tACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTtgtgtg    <  1:1879384/68‑1 (MQ=255)

                                                           tACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTtgtgtg    <  1:393366/68‑1 (MQ=255)

                                                           tACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTtgtgtg    <  1:20762/68‑1 (MQ=255)

                                                           tACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTtgtgtg    <  1:2107651/68‑1 (MQ=255)

                                                            aCTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAttg             >  1:1831449/1‑58 (MQ=255)

                                                            aCTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTTGTGTGtt  >  1:657687/1‑69 (MQ=255)

                                                            aCTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTTGTGTGtt  >  1:949938/1‑69 (MQ=255)

                                                            aCTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTTGTGTGtt  >  1:3344447/1‑69 (MQ=255)

                                                            aCTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTTGTGTGtt  >  1:2868161/1‑69 (MQ=255)

                                                            aCTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTTGTGTGtt  >  1:2313924/1‑69 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTTAAAATGGCTTTTTTAtgttgt                   <  1:1736708/51‑1 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGTCTTTTTTAtgttgt                   <  1:140031/51‑1 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt                   <  1:3186636/51‑1 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt                   <  1:2446753/51‑1 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt                   <  1:2264566/51‑1 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt                   <  1:198429/51‑1 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt                   <  1:1737595/51‑1 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt                   <  1:1456449/51‑1 (MQ=255)

                                                             cTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt                   <  1:1008757/51‑1 (MQ=255)

                                                              ttCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt                   <  1:3151200/50‑1 (MQ=255)

CTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTATTGTGTTGTGTGTT  >  minE/1512969‑1513097

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