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 F169 I1 R1	59	38.6	831760	90.8%	755238	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	93,268	G→A	A73T (GCT→ACT)	yrkE →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	93,268	0	G	A	97.6%	130.1 / NA	43	A73T (GCT→ACT)	yrkE	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (18/23); total (20/23)
Fisher's exact test for biased strand distribution p-value = 4.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAATTGACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAACAAT  >  CP000730/93128‑93412

taattGACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGc                                                                                                                                           >  1:132193/1‑148 (MQ=255)

     gACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTa                                                                                                                                      >  1:312173/1‑148 (MQ=255)

     gACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTa                                                                                                                                      >  2:318897/1‑148 (MQ=255)

     gACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGAGGTAACAGAAGTCATAATGCTAGTa                                                                                                                                      >  1:214368/1‑148 (MQ=255)

       cGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTaaa                                                                                                                                    <  2:153451/148‑1 (MQ=255)

          tAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAatat                                                                                                                                 <  1:383695/148‑1 (MQ=255)

            gAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATAttt                                                                                                                               <  2:156614/148‑1 (MQ=255)

                        agTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTGACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAgg                                                                                                                   >  1:5878/1‑148 (MQ=255)

                        agTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAgg                                                                                                                   >  1:5877/1‑148 (MQ=255)

                              cATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATaa                                                                                                             >  2:251873/1‑148 (MQ=255)

                              cATTAGGACAGATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATaa                                                                                                             <  2:401826/148‑1 (MQ=255)

                               aTTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAAc                                                                                                            >  1:237154/1‑148 (MQ=255)

                               aTTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGATAAACAAGGTTATAAc                                                                                                            >  1:245093/1‑148 (MQ=255)

                               aTTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGATAGTAAATATTTAGCTAAACAAGGTTATAAc                                                                                                            >  1:135601/1‑148 (MQ=255)

                                  aGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGtt                                                                                                         <  1:47593/148‑1 (MQ=255)

                                          tCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCt                                                                                                 >  1:94571/1‑148 (MQ=255)

                                                 ttCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGAtggt                                                                                          <  1:373480/148‑1 (MQ=255)

                                                        cTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTtata                                                                                   >  1:78332/1‑148 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATGACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 <  2:216888/148‑1 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 >  1:242178/1‑148 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 <  1:360345/148‑1 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 <  2:123593/148‑1 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAAAAAAAAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 <  2:265372/148‑1 (MQ=255)

                                                                      tgaGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATgaagaa                                                                     >  2:149002/1‑148 (MQ=255)

                                                                           ttGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGaaaa                                                                <  1:54898/148‑1 (MQ=255)

                                                                           ttGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAAAGTCTTAAAGCTTTATGGTGGTTATAAAGCTTATGAAGAAGaaaa                                                                <  1:97584/148‑1 (MQ=255)

                                                                                     cAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTAt                                                      >  1:264229/1‑148 (MQ=255)

                                                                                     cAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTAt                                                      >  2:170554/1‑148 (MQ=255)

                                                                                       aTAAAGAAAAAAATAAAACCTATTAAGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGa                                                    <  1:83472/148‑1 (MQ=255)

                                                                                                aaaaTAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaaga                                           <  1:343033/148‑1 (MQ=255)

                                                                                                  aaTAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaagaag                                         <  1:106858/148‑1 (MQ=255)

                                                                                                  aaTAAAACCTATTAGGAACGGTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaagaag                                         <  1:3522/148‑1 (MQ=255)

                                                                                                   aTAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAagaaga                                        <  2:190152/148‑1 (MQ=255)

                                                                                                                       tGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTa                    <  1:11641/148‑1 (MQ=255)

                                                                                                                            aaGTGGTAGCAGAAGTGCTAAAGCTAGAGAAGATTAGGATAAGCAAGGTCATAACGTTATAAATTTTGGTAGGGGTAAGAAAGCATATGAGGAAGAAAACGAGAGTTATGAAACACAAGAAGAATATAAAAGTATAGAAATTAAAGCa               >  2:185249/1‑148 (MQ=255)

                                                                                                                            aaGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCa               >  1:211508/1‑148 (MQ=255)

                                                                                                                             aGTGGTAACAGAAGTACTAATTCTAGTAAATATTTAGCTAAAAAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              <  2:337714/148‑1 (MQ=255)

                                                                                                                             aGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATTGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              <  1:323918/148‑1 (MQ=255)

                                                                                                                             aGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              <  1:393272/148‑1 (MQ=255)

                                                                                                                             aGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              <  1:295284/148‑1 (MQ=255)

                                                                                                                                      ggAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTAGAACGTTATAAAGCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAAc     <  2:108932/147‑1 (MQ=255)

                                                                                                                                         aGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAAAAAt  >  1:75164/1‑148 (MQ=255)

                                                                                                                                         aGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTAATGACGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAACAAt  >  2:399850/1‑148 (MQ=255)

TAATTGACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAACAAT  >  CP000730/93128‑93412

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A