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	1,020,036	A→G	57.2%	D169D (GAT→GAC)	uidC ←	predicted outer membrane porin protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,020,036	0	A	G	57.2%	24.6 / 56.5	77	D169D (GAT→GAC)	uidC	predicted outer membrane porin protein
Reads supporting (aligned to +/- strand): ref base A (21/12); new base G (15/29); total (36/41)
Fisher's exact test for biased strand distribution p-value = 1.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

CATCACGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTA  >  minE/1019972‑1020096

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:2162171/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:1719023/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:2926781/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:2930691/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:2942201/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:2898120/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:2833597/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:3260714/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCaa                                                          >  1:2691027/1‑69 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCa                                                           >  1:609018/1‑68 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCa                                                           >  1:473359/1‑68 (MQ=255)

catcaCGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCa                                                           >  1:2467028/1‑68 (MQ=255)

          acaggTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGgtg                                                 >  1:2486418/4‑68 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCTCCACAGGTCAATATTTGGCGTTaa                                             <  1:1195260/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:2750992/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:2458351/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:2301708/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:2964942/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:996483/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:3009187/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:460872/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:611568/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:670095/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:74368/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:744467/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:82666/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:839597/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:1362679/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:1901670/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:1340565/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:1890363/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:2001764/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:1285253/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:1634478/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:1171178/69‑1 (MQ=255)

             ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:1822226/69‑1 (MQ=255)

             ggTTGTT‑AATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:2091030/68‑1 (MQ=255)

              gttgttGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:975180/68‑1 (MQ=255)

                 gttgAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGc                                          >  1:1025357/1‑68 (MQ=255)

                   tgAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGccc                                        <  1:2859776/68‑1 (MQ=255)

                   tgAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGccc                                        <  1:2947389/68‑1 (MQ=255)

                         aGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAAc                                  >  1:1324688/1‑68 (MQ=255)

                             cATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa                                             <  1:3160055/53‑1 (MQ=255)

                             cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt                             >  1:1045692/1‑69 (MQ=255)

                             cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt                             >  1:57442/1‑69 (MQ=255)

                             cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt                             >  1:2810701/1‑69 (MQ=255)

                             cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt                             >  1:1721226/1‑69 (MQ=255)

                                       cTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCa                    >  1:839718/1‑68 (MQ=255)

                                       cTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCa                    >  1:2366328/1‑68 (MQ=255)

                                          gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa                              <  1:184018/55‑1 (MQ=255)

                                          gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa                              <  1:1859870/55‑1 (MQ=255)

                                          gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa                              <  1:2445616/55‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:1509602/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:580172/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:915501/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:704601/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:816/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:109325/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:1824142/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:1565901/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:2685249/69‑1 (MQ=255)

                                                      ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg    <  1:1747893/69‑1 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCt                       >  1:3366341/1‑48 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:1613192/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:2038235/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:2038991/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:962575/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:2245930/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:2417925/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:1784359/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:686073/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:1292686/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:1554046/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:3146949/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:1503713/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa  >  1:487356/1‑69 (MQ=255)

                                                        ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTACTTCAGAAACTGTCgg         >  1:1503286/1‑62 (MQ=255)

CATCACGAATACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTA  >  minE/1019972‑1020096

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