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	1,357,304	A→C	29.9%	G606G (GGT→GGG)	yehB ←	predicted outer membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,357,304	0	A	C	29.9%	67.5 / 44.1	67	G606G (GGT→GGG)	yehB	predicted outer membrane protein
Reads supporting (aligned to +/- strand): ref base A (13/34); new base C (11/9); total (24/43)
Fisher's exact test for biased strand distribution p-value = 5.06e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

GGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGAGGCAAACCC  >  minE/1357247‑1357369

ggTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGa                                                         <  1:1495713/68‑1 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACt                                                      >  1:127662/1‑68 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     <  1:1859435/69‑1 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     >  1:1055081/1‑69 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     <  1:1680940/69‑1 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     >  1:123746/1‑69 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     >  1:3114177/1‑69 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     >  1:3408344/1‑69 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     <  1:3122348/69‑1 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     <  1:3089455/69‑1 (MQ=255)

   cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg                                                     <  1:1364666/69‑1 (MQ=255)

      aTTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGAt                                                   <  1:2741661/68‑1 (MQ=255)

      aTTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGAt                                                   <  1:1967859/68‑1 (MQ=255)

      aTTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGAt                                                   <  1:1994213/68‑1 (MQ=255)

      aTTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGAt                                                   <  1:500237/68‑1 (MQ=255)

      aTTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGAt                                                   <  1:616457/68‑1 (MQ=255)

       ttCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGAt                                                   <  1:1310331/67‑1 (MQ=255)

        tCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:3291440/69‑1 (MQ=255)

        tCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:1555283/69‑1 (MQ=255)

        tCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:221375/69‑1 (MQ=255)

            cccAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATCCCGACt                                            <  1:3068311/69‑1 (MQ=255)

                gCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCt                                        <  1:1888516/69‑1 (MQ=255)

                gCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCt                                        <  1:1591116/69‑1 (MQ=255)

                 cTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTa                                       <  1:1739092/69‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:1815913/68‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:1693352/68‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:3132825/68‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:3219998/68‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:3241475/68‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:1253966/68‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:2359727/68‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:2590596/68‑1 (MQ=255)

                        ttCATTTCCCTGATACTGATAACTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTc                                 <  1:288081/68‑1 (MQ=255)

                             ttCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGAt                            <  1:2454205/68‑1 (MQ=255)

                                 cTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGAt                            <  1:2308505/64‑1 (MQ=255)

                                       ttGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:102531/38‑1 (MQ=255)

                                       ttGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:2936865/38‑1 (MQ=255)

                                       ttGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:859506/38‑1 (MQ=255)

                                       ttGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:1298689/38‑1 (MQ=255)

                                       ttGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:2812197/38‑1 (MQ=255)

                                       ttGATGACTCAGGTTGACACCATAATTGAACTGATccc                                                <  1:2009340/38‑1 (MQ=255)

                                         gatgaCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGtatta                >  1:902569/1‑68 (MQ=255)

                                         gatgaCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGtatta                >  1:512350/1‑68 (MQ=255)

                                         gatgaCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGtatta                >  1:1990382/1‑68 (MQ=255)

                                         gatgaCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGtat                  <  1:1169715/66‑1 (MQ=255)

                                         gatgaCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTACTGATAATCCCGtattat               >  1:323929/1‑69 (MQ=255)

                                         gatgaCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTACTGATAATCCCGtattat               >  1:319813/1‑69 (MQ=255)

                                             aCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGa           >  1:1478538/1‑69 (MQ=255)

                                             aCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGa           >  1:393037/1‑69 (MQ=255)

                                             aCTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGa           >  1:1579032/1‑69 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCtt                                           >  1:292841/1‑35 (MQ=16)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:398085/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:2634376/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:1059712/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:2170915/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:492450/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:3185353/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:1550407/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:302800/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCGGCTTCCAACGGTTCCTGa                             >  1:1409225/1‑50 (MQ=255)

                                              cTCAGGTTGACCCCATAGTTAAACTGATCCCAGCTTCCAACGGTTCCTGa                             >  1:1003170/1‑50 (MQ=255)

                                                   gTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGAGGCa       <  1:367024/67‑1 (MQ=255)

                                                   gTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGAGGCa       <  1:471382/67‑1 (MQ=255)

                                                   gTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGAGGCa       <  1:2961393/67‑1 (MQ=255)

                                                   gTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGAGGCa       <  1:1352351/67‑1 (MQ=255)

                                                   gTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGAGGCa       <  1:701398/67‑1 (MQ=255)

                                                      gACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGAGGCAAAccc  <  1:1328473/69‑1 (MQ=255)

GGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTGATCCCGACTCCCTACTGTTCCTGATAATCCCGTATTATTTGAGGCAAACCC  >  minE/1357247‑1357369

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