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	2,434,343	A→G	38.8%	intergenic (+95/‑41)	rhlB → / → gpp	ATP‑dependent RNA helicase/guanosine pentaphosphatase/exopolyphosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,434,343	0	A	G	38.8%	60.5 / 82.6	121	intergenic (+95/‑41)	rhlB/gpp	ATP‑dependent RNA helicase/guanosine pentaphosphatase/exopolyphosphatase
Reads supporting (aligned to +/- strand): ref base A (45/29); new base G (26/21); total (71/50)
Fisher's exact test for biased strand distribution p-value = 5.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-01

Only 100 of 127 total aligned reads displayed.

CAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCACCTCGTCGCTGTATGC  >  minE/2434276‑2434409

   aCTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGaa                                                                 <  1:1105307/68‑1 (MQ=255)

   aCTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGaa                                                                 <  1:3011308/68‑1 (MQ=255)

         tCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGcc                                                          >  1:880265/1‑69 (MQ=255)

         tCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGc                                                           >  1:2491450/1‑68 (MQ=255)

                 gCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACaga                                                  >  1:3369359/1‑69 (MQ=255)

                   aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                                                <  1:1528210/69‑1 (MQ=255)

                   aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                                                <  1:226303/69‑1 (MQ=255)

                   aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                                                <  1:2037698/69‑1 (MQ=255)

                   aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                                                <  1:936750/69‑1 (MQ=255)

                      ataatgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:2793406/67‑1 (MQ=255)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAGCGCAGAGACAg                                             <  1:2243906/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:3231795/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:1737892/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:1681708/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:2970746/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:1889647/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:3214674/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:3406069/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:238409/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:725034/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:12904/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:751995/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:247510/69‑1 (MQ=38)

                      agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                                             <  1:780215/69‑1 (MQ=38)

                        aatgaatCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                                                <  1:327278/64‑1 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCTGGTGAAGGaa                                                                 >  1:316690/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:2121289/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:1064655/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:2208510/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:3010971/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:2906564/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:2871977/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:2658380/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:1962081/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:1124526/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:3402817/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:173364/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:1659254/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:1615603/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:1171911/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:499498/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:3013196/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:1250758/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                                                 >  1:577971/1‑45 (MQ=255)

                          tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGa                                                                  >  1:2868018/1‑44 (MQ=38)

                              tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg                                      <  1:2356100/68‑1 (MQ=255)

                              tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg                                      <  1:410314/68‑1 (MQ=255)

                              tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg                                      <  1:1818730/68‑1 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:2849263/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:949083/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:2651011/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:1809457/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:2113112/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:1310273/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:2220045/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:1353040/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:2403281/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                                              >  1:1341376/1‑58 (MQ=255)

                                ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGa                                    >  1:692307/1‑68 (MQ=255)

                                      aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag                             >  1:1127036/1‑69 (MQ=255)

                                      aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag                             <  1:1762841/69‑1 (MQ=255)

                                      aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag                             >  1:355976/1‑69 (MQ=255)

                                      aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag                             <  1:581143/69‑1 (MQ=255)

                                      aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag                             <  1:1075338/69‑1 (MQ=255)

                                      aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGAAAGATTGAAGGATGAagag                             <  1:3367763/69‑1 (MQ=255)

                                                agtaAGTGATTGAGGTGTTAGATTGCTGCCTACACAGAGACAGTTTGAAg                                      <  1:1178443/50‑1 (MQ=255)

                                                 gtaAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTcc                   >  1:585108/1‑68 (MQ=255)

                                                 gtaAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTcc                   <  1:206323/68‑1 (MQ=255)

                                                 gtaAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCa                  >  1:2898329/1‑69 (MQ=255)

                                                 gtaAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCa                  >  1:498293/1‑69 (MQ=255)

                                                 gtaAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCa                  >  1:22606/1‑69 (MQ=255)

                                                 gtaAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCa                  >  1:2439278/1‑69 (MQ=255)

                                                 gtaAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCa                  >  1:2671338/1‑69 (MQ=255)

                                                 gtaAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCa                  >  1:3192805/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAcc                >  1:1499542/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAcc                >  1:1518460/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAcc                >  1:769451/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAcc                >  1:1030690/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAcc                >  1:335539/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAcc                >  1:2590968/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAcc                >  1:1084056/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAcc                >  1:2696027/1‑69 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAc                 <  1:320093/68‑1 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAc                 >  1:2567441/1‑68 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAc                 <  1:908893/68‑1 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAc                 >  1:2888106/1‑68 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAc                 <  1:2326273/68‑1 (MQ=255)

                                                   aaGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCAc                 <  1:2785989/68‑1 (MQ=255)

                                                    aGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag                             >  1:181030/1‑55 (MQ=255)

                                                    aGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag                             >  1:66070/1‑55 (MQ=255)

                                                    aGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATCAagag                             >  1:2341955/1‑55 (MQ=255)

                                                     gTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg                                      <  1:2896686/45‑1 (MQ=255)

                                                       gATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCACCtcgt            >  1:2540678/1‑69 (MQ=255)

                                                              gTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCACCTCGTCGCTGTa     <  1:2087654/69‑1 (MQ=255)

                                                               tGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag                             <  1:1816564/44‑1 (MQ=255)

                                                                gAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCACCTCGTCGCTGt      >  1:2644870/1‑66 (MQ=255)

                                                                 aaaGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGATTATGGGTTCCACCTCGTCGCTTTATGc  >  1:2805540/1‑69 (MQ=255)

                                                                 aaaGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCACCTCGTCGCTGTATGc  >  1:851221/1‑69 (MQ=255)

                                                                 aaaGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCACCTCGTCGCTGTATGc  >  1:2227478/1‑69 (MQ=255)

                                                                 aaaGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCACCTCGTCGCTGTATGc  >  1:2286228/1‑69 (MQ=255)

CAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAGTATGGGTTCCACCTCGTCGCTGTATGC  >  minE/2434276‑2434409

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A