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	572,255	G→A	26.1%	I164I (ATC→ATT)	aqpZ ←	aquaporin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	572,255	0	G	A	26.1%	70.2 / 20.8	61	I164I (ATC→ATT)	aqpZ	aquaporin
Reads supporting (aligned to +/- strand): ref base G (31/14); new base A (13/3); total (44/17)
Fisher's exact test for biased strand distribution p-value = 5.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

GTTAACAGAAGTGTTAGTCACCGGAATACTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAACCTGCA  >  minE/572189‑572321

gTTAACGGAAGTGTTAGTCACCGGAATACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAAt                                                                  <  1:1157276/69‑1 (MQ=255)

gTTAACGGAAGTGTTAGTCACCGGAATACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAAt                                                                  <  1:2581928/69‑1 (MQ=255)

gTTAACGGAAGTGTTAGTCACCGGAATACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAAt                                                                  <  1:1428513/69‑1 (MQ=255)

 ttAACAGAAGTGTTAGTCACCGGAATACTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGAt                                                                  >  1:3208379/1‑68 (MQ=255)

 ttAACAGAAGTGTTAGTCACCGGAATACTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGATc                                                                 >  1:333286/1‑69 (MQ=255)

            gtTAGTCACCGGAATACTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCAGCGCAAAAcc                                                      >  1:1980053/1‑69 (MQ=255)

                        aaTACTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGaa                                          <  1:2623768/69‑1 (MQ=255)

                        aaTACTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGaa                                          <  1:1435480/69‑1 (MQ=255)

                        aaTACTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGaa                                          <  1:1948636/69‑1 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGaa                                          >  1:3009856/1‑68 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGaa                                          >  1:948065/1‑68 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGaa                                          >  1:2063640/1‑68 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGaa                                          >  1:1992461/1‑68 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:2804589/1‑69 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:2518255/1‑69 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:3360277/1‑69 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:444566/1‑69 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:1480765/1‑69 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:857902/1‑69 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:1178516/1‑69 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:1209389/1‑69 (MQ=255)

                         aTACTGATTAAGTGAATCAGGGTTAAGGCCAGACCAATGGCAATTGGCGCAAAACCAGCAGGAGCGAAt                                         >  1:1186120/1‑69 (MQ=255)

                            cTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTg                                      >  1:2918117/1‑69 (MQ=255)

                                  aaGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGtt                                >  1:1619151/1‑69 (MQ=255)

                                  aaGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGtt                                >  1:968939/1‑69 (MQ=255)

                                  aaGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGtt                                >  1:2215747/1‑69 (MQ=255)

                                  aaGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGtt                                >  1:3070121/1‑69 (MQ=255)

                                  aaGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGtt                                >  1:2978187/1‑69 (MQ=255)

                                  aaGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGtt                                >  1:24404/1‑69 (MQ=255)

                                           aGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTgg                       <  1:2581630/69‑1 (MQ=255)

                                           aGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTgg                       <  1:2956806/69‑1 (MQ=255)

                                           aGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTgg                       <  1:3081152/69‑1 (MQ=255)

                                           aGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTgg                       <  1:607893/69‑1 (MQ=255)

                                           aGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTgg                       <  1:3288176/69‑1 (MQ=255)

                                                tAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCa                   >  1:2894779/1‑68 (MQ=255)

                                                tAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCa                   >  1:2528056/1‑68 (MQ=255)

                                                tAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCa                   >  1:1781348/1‑68 (MQ=255)

                                                tAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGAACa                   >  1:1633817/1‑68 (MQ=255)

                                                      cAGACCTATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACa             >  1:439926/1‑68 (MQ=255)

                                                      cAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGcc                           >  1:597574/1‑54 (MQ=255)

                                                      cAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAAc              >  1:2222968/1‑67 (MQ=255)

                                                      cAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACa             >  1:1042165/1‑68 (MQ=255)

                                                      cAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACa             >  1:1685382/1‑68 (MQ=255)

                                                         aCCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGaa         <  1:1338563/69‑1 (MQ=255)

                                                         aCCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGaa         <  1:778045/69‑1 (MQ=255)

                                                         aCCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGaa         <  1:772804/69‑1 (MQ=255)

                                                         aCCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGaa         <  1:2304519/69‑1 (MQ=255)

                                                         aCCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGaa         <  1:2693000/69‑1 (MQ=255)

                                                         aCCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGGTGCGCCGTGGATCACCAACAGGaa         <  1:909248/69‑1 (MQ=255)

                                                          ccAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGTaaa        >  1:2183793/1‑69 (MQ=255)

                                                          ccAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGaaa        >  1:3258252/1‑69 (MQ=255)

                                                             aTAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAAcc      >  1:3139111/1‑68 (MQ=255)

                                                             aTAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAAcc      >  1:90364/1‑68 (MQ=255)

                                                             aTAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAAc       >  1:1071822/1‑67 (MQ=255)

                                                               aGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAACCTGc   >  1:3008202/1‑69 (MQ=255)

                                                                gCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAAcc      >  1:2631182/1‑65 (MQ=255)

                                                                gCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAACCTGCa  >  1:141931/1‑69 (MQ=255)

                                                                gCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAACCTGCa  >  1:1453287/1‑69 (MQ=255)

                                                                gCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAACCTGCa  >  1:178354/1‑69 (MQ=255)

                                                                gCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAACCTGCa  >  1:2104001/1‑69 (MQ=255)

                                                                gCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAACCTGCa  >  1:2366115/1‑69 (MQ=255)

GTTAACAGAAGTGTTAGTCACCGGAATACTAATTAAGTGAATCAGGGTTAAGGCCAGACCAATAGCGATCGGCGCAAAACCTGCCGGCGCGAATTTGTCGGTTGCGCCGTGGATCACCAACAGGAAACCTGCA  >  minE/572189‑572321

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