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 F3 I0 R2	232	76.3	4135488	90.9%	3759158	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,026,348	T→C	25.7%	E175G (GAG→GGG)	malI ←	DNA‑binding transcriptional repressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,026,348	0	T	C	25.7%	118.5 / 48.0	70	E175G (GAG→GGG)	malI	DNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand): ref base T (25/27); new base C (9/9); total (34/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

GCACGGGTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATAACT  >  minE/1026279‑1026412

gCACGGGTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTc                                                                 >  1:2289952/1‑71 (MQ=255)

   cGGGTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGt                                                              >  1:3802429/1‑71 (MQ=255)

   cGGGTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGt                                                              >  1:3809990/1‑71 (MQ=255)

   cGGGTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGt                                                              >  1:1681176/1‑71 (MQ=255)

       ttAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:9010/71‑1 (MQ=255)

       ttAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:3332150/71‑1 (MQ=255)

       ttAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:1193827/71‑1 (MQ=255)

             aGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACtgt                                                    >  1:5905/1‑71 (MQ=255)

              ggAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACtgtg                                                   <  1:1783477/71‑1 (MQ=255)

                 aCTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAg                                                >  1:1585760/1‑71 (MQ=255)

                 aCTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAg                                                >  1:2862742/1‑71 (MQ=255)

                    ttGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCt                                             >  1:2912141/1‑71 (MQ=255)

                    ttGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCt                                             >  1:3073712/1‑71 (MQ=255)

                    ttGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCt                                             >  1:2341898/1‑71 (MQ=255)

                    ttGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCt                                             >  1:3199929/1‑71 (MQ=255)

                     tGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaacaa                                                        >  1:3973546/1‑59 (MQ=255)

                     tGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaacaa                                                        >  1:4021642/1‑59 (MQ=255)

                         cTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAg                                                <  1:2792432/63‑1 (MQ=255)

                            ccagccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCAtgttg                                     <  1:1249739/71‑1 (MQ=255)

                              agccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaaca                                                         >  1:1860546/1‑49 (MQ=255)

                              agccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaaca                                                         >  1:2671044/1‑49 (MQ=255)

                              agccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaaca                                                         >  1:3566905/1‑49 (MQ=255)

                              agccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaaca                                                         >  1:2215361/1‑49 (MQ=255)

                              agccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaaca                                                         >  1:810807/1‑49 (MQ=255)

                              agccagGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaaca                                                         >  1:2639166/1‑49 (MQ=255)

                                  agGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaaca                                                         <  1:570329/45‑1 (MQ=255)

                                  agGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaaca                                                         <  1:3685970/45‑1 (MQ=255)

                                   ggCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:1117262/43‑1 (MQ=255)

                                   ggCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:3529230/43‑1 (MQ=255)

                                   ggCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:738691/43‑1 (MQ=255)

                                   ggCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:2669062/43‑1 (MQ=255)

                                   ggCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:1158154/43‑1 (MQ=255)

                                   ggCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:1920745/43‑1 (MQ=255)

                                   ggCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:1994345/43‑1 (MQ=255)

                                    gCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:2036313/42‑1 (MQ=255)

                                    gCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTcaac                                                          <  1:3281870/42‑1 (MQ=255)

                                         ccGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCg                        >  1:173059/1‑71 (MQ=255)

                                          cGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCAGCATGTTGTCCGGGCGAACCg                        >  1:3718180/1‑70 (MQ=255)

                                          cGCTGATGCCCATTGCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCg                        >  1:1018610/1‑70 (MQ=255)

                                               aTGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATc                    <  1:273679/69‑1 (MQ=255)

                                                     aTTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAAcatcat            >  1:3878281/1‑71 (MQ=255)

                                                      ttGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGa                            <  1:4087396/54‑1 (MQ=255)

                                                      ttGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGa                            <  1:2835834/54‑1 (MQ=255)

                                                      ttGCGAATGAGATGCTCCGTCAACAACTGTGCAGACTGCATGTTGTCCGGGCGa                            <  1:526350/54‑1 (MQ=255)

                                                       tGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCaa                  >  1:26263/1‑63 (MQ=255)

                                                        gCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACatcatc           >  1:1219760/1‑69 (MQ=255)

                                                        gCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACatcatc           >  1:156952/1‑69 (MQ=255)

                                                        gCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGG‑‑GAACCGTATCAACATCATCAAg        <  1:3796741/70‑1 (MQ=255)

                                                        gCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCAtgttgt                                    >  1:1268166/1‑44 (MQ=255)

                                                        gCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACatcatc           >  1:2766519/1‑69 (MQ=255)

                                                        gCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACatcatc           >  1:1524614/1‑69 (MQ=255)

                                                        gCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACatcatc           >  1:3111235/1‑69 (MQ=255)

                                                        gCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACatcatc           >  1:2329281/1‑69 (MQ=255)

                                                        gCGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACatcatc           >  1:3263402/1‑69 (MQ=255)

                                                         cGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg        <  1:2520512/71‑1 (MQ=255)

                                                         cGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg        <  1:2455631/71‑1 (MQ=255)

                                                         cGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg        <  1:2136558/71‑1 (MQ=255)

                                                         cGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg        <  1:3597414/71‑1 (MQ=255)

                                                         cGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg        <  1:2328823/71‑1 (MQ=255)

                                                         cGAATGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAg        <  1:3515791/71‑1 (MQ=255)

                                                          gAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCAtgttg                                     <  1:1271128/41‑1 (MQ=255)

                                                           aaTGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGAt      <  1:491190/71‑1 (MQ=255)

                                                           aaTGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGAt      <  1:3088400/71‑1 (MQ=255)

                                                           aaTGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGAt      <  1:884375/71‑1 (MQ=255)

                                                           aaTGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGAt      <  1:260589/71‑1 (MQ=255)

                                                            aTGAGATGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGAt      >  1:2467470/1‑70 (MQ=255)

                                                             tGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATaa    >  1:4037015/1‑71 (MQ=255)

                                                               agaTGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATAAc   <  1:590456/70‑1 (MQ=255)

                                                               agaTGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATAAc   <  1:3582209/70‑1 (MQ=255)

                                                               agaTGCCCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATAACt  <  1:552990/71‑1 (MQ=255)

GCACGGGTTAATGAGGAACTTTGCCCTCCCAGCCAGGCGATCCGCTGATGCCCATTGCGAATGAGATGCTCCGTCAACAACTGTGCAGCCTGCATGTTGTCCGGGCGAACCGTATCAACATCATCAAGATAACT  >  minE/1026279‑1026412

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