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
A1 F104 I1 R1	32	52.7	1196080	90.6%	1083648	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,125,066	G→C	E729Q (GAG→CAG)	pycA →	pyruvate carboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,125,066	0	G	C	96.0%	160.3 / NA	50	E729Q (GAG→CAG)	pycA	pyruvate carboxylase
Reads supporting (aligned to +/- strand): ref base G (1/1); new base C (19/29); total (20/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGCGATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTGAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTT  >  CP000730/1124931‑1125201

gAGCGATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTa                                                                                                                                    >  1:267969/1‑141 (MQ=255)

     aTCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCTATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATc                                                                                                                               <  1:829314/141‑1 (MQ=255)

     aTCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATc                                                                                                                               <  1:1041953/141‑1 (MQ=255)

        aaaCATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGc                                                                                                                            >  1:1077987/1‑141 (MQ=255)

                   cTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTATCGGTTAAAGATCTGGCAGGCCTATTAACACTTAAAGCCGCATACGAATGGCTTGGTGAGGTAAAATTAGcgtgaggtttga                                                                                                                 >  1:399861/1‑130 (MQ=255)

                   cTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTAc                                                                                                                 >  1:1006979/1‑141 (MQ=255)

                      tAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCaa                                                                                                              <  1:974010/141‑1 (MQ=255)

                       agagTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAAt                                                                                                             <  1:968492/141‑1 (MQ=255)

                               atGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTc                                                                                                     <  1:560562/141‑1 (MQ=255)

                                tGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTca                                                                                                    <  1:904901/141‑1 (MQ=255)

                                tGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTca                                                                                                    <  1:904933/141‑1 (MQ=255)

                                tGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTca                                                                                                    <  1:387800/141‑1 (MQ=255)

                                 gTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTATATTTACCAATTCATCTTcac                                                                                                   >  1:211943/1‑141 (MQ=255)

                                      aCTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATAATCTAGCTATTAAATATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCa                                                                                              <  1:920596/141‑1 (MQ=255)

                                        gaGCTAAAGAGTTAGAACGTGAAGGTTGCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATg                                                                                            <  1:244147/140‑1 (MQ=255)

                                         aGCTAAAGAGTTAGACCGGGAAGGTTTCCATATTTTAGCGATTAAAGCTATGGCAGGCTTATTACAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGa                                                                                           <  1:237276/141‑1 (MQ=255)

                                         aGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATGTTCACACTCATGa                                                                                           >  1:1078919/1‑141 (MQ=255)

                                         aGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGa                                                                                           <  1:1087595/141‑1 (MQ=255)

                                           cTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATa                                                                                         >  1:506529/1‑141 (MQ=255)

                                            tAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATAc                                                                                        <  1:398175/141‑1 (MQ=255)

                                             aaaGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACa                                                                                       <  1:196533/141‑1 (MQ=255)

                                              aaGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCATTTCATCTTCACACTCATGATACaa                                                                                      <  1:766889/141‑1 (MQ=255)

                                                 agtcaGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTg                                                                                   <  1:644082/137‑1 (MQ=255)

                                                 agTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTGAGTTAAAATCAGCTGTAGATTTACCTATTCATCTTCACACTCATGATACAAGTg                                                                                   <  1:773357/141‑1 (MQ=255)

                                                 agTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTg                                                                                   <  1:201154/141‑1 (MQ=255)

                                                   ttAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTggg                                                                                 >  1:104405/1‑140 (MQ=255)

                                                   ttAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGt                                                                                 >  1:1027783/1‑141 (MQ=255)

                                                    tAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTa                                                                                <  1:1068998/141‑1 (MQ=255)

                                                    tAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTa                                                                                >  1:219335/1‑141 (MQ=255)

                                                      gAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCCCACTCATGATACAAGTGGTAAt                                                                              >  1:203122/1‑141 (MQ=255)

                                                        aCGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATgg                                                                            <  1:1064300/141‑1 (MQ=255)

                                                        aCGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATgg                                                                            >  1:1156236/1‑141 (MQ=255)

                                                        aCGTGAAGGGTTCCATATCTTAGCGATTAAATATAGGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCCGTAGATTTACCAATTCAGCTTCACACTCATGATACAAGTGGTAATgg                                                                            <  1:279420/141‑1 (MQ=255)

                                                        aCGTGAAGATTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATgg                                                                            <  1:1064349/141‑1 (MQ=255)

                                                         cGTGAAGGCTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGt                                                                           <  1:71232/141‑1 (MQ=255)

                                                            gAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTGAAAGCTAAAGCCGCGGACGAAAAGATTTGACAGTTCAACCATGCAGGTGTTTTAGCAATTCATCTTGACACGTCTGATACAAATgggcagggtgta                                                                        >  1:519616/1‑131 (MQ=255)

                                                            gAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTtta                                                                        >  1:674342/1‑141 (MQ=255)

                                                                   tCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACAt                                                                 <  1:633483/141‑1 (MQ=255)

                                                                     cATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCACCTTAACACTCATGATACAACTGGTAATGGTGTATTTACaaaa                                                               >  1:1045643/1‑138 (MQ=255)

                                                                                       aatatGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCATACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCt                                             <  1:794129/140‑1 (MQ=255)

                                                                                        atatGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACACGCAATAGATGCTg                                            >  1:88678/1‑141 (MQ=255)

                                                                                         tatGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACCAACACGCAATAGATGCTgg                                           <  1:658082/141‑1 (MQ=255)

                                                                                                            ccgaaaGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCAACTTCACACTCATGATACAAGGGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATAct                        <  1:344228/138‑1 (MQ=255)

                                                                                                            ccTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATAct                        >  1:590747/1‑141 (MQ=255)

                                                                                                            ccTAAAGACGCTTACGAATTGAGTGGTCAGTCAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATAct                        <  1:430370/141‑1 (MQ=255)

                                                                                                                   ccGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCAGTTg                 >  1:189956/1‑141 (MQ=255)

                                                                                                                         aCGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCaa           <  1:1110747/141‑1 (MQ=255)

                                                                                                                              tagactgGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGt      <  1:406449/136‑1 (MQ=255)

                                                                                                                                  ttgGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGtt  >  1:688794/1‑141 (MQ=255)

                                                                                                                                  ttgGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATAAAGGCCCTAACAAGCAATAGATGCTGGTGTCGATATCATTGATACGGCTGTTGCTTCAAAGAGTGGtt  >  1:1171911/1‑141 (MQ=255)

GAGCGATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTGAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTT  >  CP000730/1124931‑1125201

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A