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
A5 F17 I0 R2	162	60.6	4616657	98.5%	4547407	62.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,333,478	G→A	9.7%	R555H (CGC→CAC)	yjdA →	conserved hypothetical protein with nucleoside triphosphate hydrolase domain

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,333,478	0	G	A	9.7%	190.4 / 8.9	62	R555H (CGC→CAC)	yjdA	conserved hypothetical protein with nucleoside triphosphate hydrolase domain
Reads supporting (aligned to +/- strand): ref base G (25/31); new base A (2/4); total (27/35)
Fisher's exact test for biased strand distribution p-value = 6.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

AGTCGCGACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCATTTTCC  >  W3110S.gb/4333408‑4333544

aGTCGCTACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCg                                                                    >  1:1214508/1‑71 (MQ=255)

   cgcgACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGccc                                                                 >  1:1988134/1‑71 (MQ=255)

    gcgACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGccc                                                                 <  1:4329898/70‑1 (MQ=255)

     cgACTTTACGCTGCGTTTTGCCGAGCTTGAATGCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCa                                                               <  1:4560462/71‑1 (MQ=255)

      gACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCAt                                                              >  1:2189815/1‑71 (MQ=255)

       aCTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCACCCCAtt                                                             <  1:4355728/71‑1 (MQ=255)

        cTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCAtt                                                             >  1:2372457/1‑70 (MQ=255)

          ttACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAg                                                          >  1:1441700/1‑71 (MQ=255)

           tACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGa                                                           <  1:3633364/69‑1 (MQ=255)

           tACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAg                                                          >  1:4053969/1‑70 (MQ=255)

            aCGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGc                                                         >  1:2275541/1‑70 (MQ=255)

                    ttttGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCG‑CCCATTGAGCAACAAGTCaa                                               <  1:1409304/71‑1 (MQ=255)

                      ttGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCaa                                               <  1:4056550/70‑1 (MQ=255)

                       tGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCaaa                                              <  1:4388894/70‑1 (MQ=255)

                         ccGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAAt                                            <  1:130524/70‑1 (MQ=255)

                          cGAGCTTGAATCCACCCTTTGCCTGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATgg                                          <  1:3642938/71‑1 (MQ=255)

                          cGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATgg                                          <  1:3965289/71‑1 (MQ=255)

                          cGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATgg                                          <  1:2034335/71‑1 (MQ=255)

                           gAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATgg                                          >  1:2948583/1‑70 (MQ=255)

                            aGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGaa                                        <  1:1463171/71‑1 (MQ=255)

                               ttGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAAt                                            <  1:1519591/64‑1 (MQ=255)

                                tGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAAtt                                      >  1:1693812/1‑69 (MQ=255)

                                 gAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAg                                                          >  1:4247580/1‑48 (MQ=255)

                                 gAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAg                                   >  1:4203169/1‑71 (MQ=255)

                                 gAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAg                                   >  1:1658570/1‑71 (MQ=255)

                                  aaTCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGc                                  <  1:3417675/71‑1 (MQ=255)

                                  aaTCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGc                                  <  1:3858892/71‑1 (MQ=255)

                                   aTCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGc                                  >  1:4168946/1‑70 (MQ=255)

                                     ccACCCTTTGCCGGGTGTTAACCGATGTTATTCACCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAg                               >  1:3314582/1‑71 (MQ=255)

                                      cACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGcaaca                                                     <  1:2790634/48‑1 (MQ=255)

                                      cACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGcaac                                                      <  1:63891/47‑1 (MQ=255)

                                       aCCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGa                                                           <  1:362459/41‑1 (MQ=255)

                                       aCCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGa                                                           <  1:2290568/41‑1 (MQ=255)

                                       aCCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTc                             <  1:3325024/71‑1 (MQ=255)

                                        cccTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGc                                                         <  1:624907/42‑1 (MQ=255)

                                        cccTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCa                            <  1:3357198/71‑1 (MQ=255)

                                            ttGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGa                                    >  1:4576645/1‑59 (MQ=255)

                                             tGCCGGGTGTTGACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGtt                       >  1:134643/1‑71 (MQ=255)

                                             tGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGcaacaa                                                    >  1:3256856/1‑42 (MQ=255)

                                             tGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAggg                         <  1:503026/69‑1 (MQ=255)

                                             tGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGt                        <  1:3884254/70‑1 (MQ=255)

                                             tGCCGGGTGTTAACCGATGTTATTCACCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGt                        <  1:3778548/70‑1 (MQ=255)

                                              gCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGtt                       <  1:162403/70‑1 (MQ=255)

                                                  ggTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTc                  >  1:2272088/1‑71 (MQ=255)

                                                   gtgtTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTcc                 <  1:3792177/71‑1 (MQ=255)

                                                   gtgtTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTcc                 <  1:3908375/71‑1 (MQ=255)

                                                    tgtTAACCGATGTTATTCGCCCCATTGAGCAACAATTCAAAATGGa                                         <  1:303172/46‑1 (MQ=255)

                                                    tgtTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCa                                                <  1:514442/39‑1 (MQ=255)

                                                    tgtTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTcc                 <  1:2869222/70‑1 (MQ=255)

                                                      ttAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGt                        >  1:2850001/1‑61 (MQ=255)

                                                      ttAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTg               <  1:1788042/70‑1 (MQ=255)

                                                      ttAACCGATGTTATTCACCCCATTGAGCAACAAGTCAAAATGGa                                         <  1:146201/44‑1 (MQ=255)

                                                       tAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTc                  >  1:1206400/1‑66 (MQ=255)

                                                        aaCCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGaa                                        >  1:2960102/1‑43 (MQ=255)

                                                        aaCCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGa                                    >  1:21764/1‑47 (MQ=255)

                                                           cGATGTTATTCACCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTg               >  1:1708755/1‑65 (MQ=255)

                                                             aTGTTATTCGCCCAATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCAt       >  1:3866119/1‑71 (MQ=255)

                                                              tGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTgg              >  1:3756186/1‑63 (MQ=255)

                                                                ttATTCACCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCAttt     <  1:2836761/70‑1 (MQ=255)

                                                                  aTTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGa                                    >  1:1215430/1‑37 (MQ=255)

                                                                  aTTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCATTTTcc  >  1:1863234/1‑71 (MQ=255)

                                                                    tCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCa                            <  1:3591559/43‑1 (MQ=255)

                                                                    tCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCt                >  1:3662699/1‑55 (MQ=255)

AGTCGCGACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCATTTTCC  >  W3110S.gb/4333408‑4333544

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