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	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	93,268	G→A	A73T (GCT→ACT)	glpE →	Thiosulfate sulfurtransferase GlpE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	93,268	0	G	A	97.9%	162.2 / NA	49	A73T (GCT→ACT)	glpE	Thiosulfate sulfurtransferase GlpE
Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (20/27); total (22/27)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAATTGACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAACAAT  >  USA300TCH1516_ALE/93128‑93412

taattGACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGc                                                                                                                                           >  3:132193/1‑148 (MQ=255)

     gACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTa                                                                                                                                      >  4:318897/1‑148 (MQ=255)

     gACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTa                                                                                                                                      >  3:312173/1‑148 (MQ=255)

     gACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGAGGTAACAGAAGTCATAATGCTAGTa                                                                                                                                      >  3:214368/1‑148 (MQ=255)

       cGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTaaa                                                                                                                                    <  4:153451/148‑1 (MQ=255)

        gTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCt                                                                                                                                          <  1:1011/141‑1 (MQ=255)

          tAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAatat                                                                                                                                 <  3:383695/148‑1 (MQ=255)

            gAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATAttt                                                                                                                               <  4:156614/148‑1 (MQ=255)

                        agTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTGACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAgg                                                                                                                   >  3:5878/1‑148 (MQ=255)

                        agTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAgg                                                                                                                   >  3:5877/1‑148 (MQ=255)

                              cATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATaa                                                                                                             >  4:251873/1‑148 (MQ=255)

                              cATTAGGACAGATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATaa                                                                                                             <  4:401826/148‑1 (MQ=255)

                               aTTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAAc                                                                                                            >  3:237154/1‑148 (MQ=255)

                               aTTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGATAAACAAGGTTATAAc                                                                                                            >  3:245093/1‑148 (MQ=255)

                               aTTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGATAGTAAATATTTAGCTAAACAAGGTTATAAc                                                                                                            >  3:135601/1‑148 (MQ=255)

                                  aGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGtt                                                                                                         <  3:47593/148‑1 (MQ=255)

                                          tCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCt                                                                                                 >  3:94571/1‑148 (MQ=255)

                                                 ttCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGAtggt                                                                                          <  3:373480/148‑1 (MQ=255)

                                                        cTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTtata                                                                                   >  3:78332/1‑148 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATGACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 <  4:216888/148‑1 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGAtggtgg                                                                                        <  1:45148/141‑1 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 <  4:123593/148‑1 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 >  3:242178/1‑148 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 <  3:360345/148‑1 (MQ=255)

                                                          tCATCCTGTTGATGAGATTGAGTCATTCAAAAAAAAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                                 <  4:265372/148‑1 (MQ=255)

                                                            acccTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGtt                                                                                      <  1:10199/139‑1 (MQ=255)

                                                                      tgaGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATgaagaa                                                                     >  4:149002/1‑148 (MQ=255)

                                                                           ttGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGaaaa                                                                <  3:54898/148‑1 (MQ=255)

                                                                           ttGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAAAGTCTTAAAGCTTTATGGTGGTTATAAAGCTTATGAAGAAGaaaa                                                                <  3:97584/148‑1 (MQ=255)

                                                                                 cATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTTATGGTGGTTATAAAGCTTATGAAGAAGaaa                                                                 >  2:37452/1‑141 (MQ=255)

                                                                                     cAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTAt                                                      >  4:170554/1‑148 (MQ=255)

                                                                                     cAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTAt                                                      >  3:264229/1‑148 (MQ=255)

                                                                                       aTAAAGAAAAAAATAAAACCTATTAAGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGa                                                    <  3:83472/148‑1 (MQ=255)

                                                                                                aaaaTAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaaga                                           <  3:343033/148‑1 (MQ=255)

                                                                                                  aaTAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaagaag                                         <  3:106858/148‑1 (MQ=255)

                                                                                                  aaTAAAACCTATTAGGAACGGTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaagaag                                         <  3:3522/148‑1 (MQ=255)

                                                                                                   aTAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAagaaga                                        <  4:190152/148‑1 (MQ=255)

                                                                                                   aTAAAACCTATGATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGGAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAGAACGATAGTTATGATacac                                               <  1:36511/141‑1 (MQ=255)

                                                                                                                       tGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTa                    <  3:11641/148‑1 (MQ=255)

                                                                                                                            aaGTGGTAGCAGAAGTGCTAAAGCTAGAGAAGATTAGGATAAGCAAGGTCATAACGTTATAAATTTTGGTAGGGGTAAGAAAGCATATGAGGAAGAAAACGAGAGTTATGAAACACAAGAAGAATATAAAAGTATAGAAATTAAAGCa               >  4:185249/1‑148 (MQ=255)

                                                                                                                            aaGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCa               >  3:211508/1‑148 (MQ=255)

                                                                                                                             aGTGGTAACAGAAGTACTAATTCTAGTAAATATTTAGCTAAAAAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              <  4:337714/148‑1 (MQ=255)

                                                                                                                             aGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATTGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              <  3:323918/148‑1 (MQ=255)

                                                                                                                             aGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              <  3:295284/148‑1 (MQ=255)

                                                                                                                             aGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              <  3:393272/148‑1 (MQ=255)

                                                                                                                                    aCAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg              >  2:1051/1‑141 (MQ=255)

                                                                                                                                      ggAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTAGAACGTTATAAAGCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAAc     <  4:108932/147‑1 (MQ=255)

                                                                                                                                         aGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAAAAAt  >  3:75164/1‑148 (MQ=255)

                                                                                                                                         aGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTAATGACGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAACAAt  >  4:399850/1‑148 (MQ=255)

TAATTGACGTTAGAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAGATCGTAAACAAT  >  USA300TCH1516_ALE/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