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
A19 F57 I0 R1	18	37.5	860368	95.0%	817349	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,373,019	G→A	36.7%	Q253* (CAG→TAG)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,373,019	0	G	A	36.7%	34.1 / 41.1	46	Q253* (CAG→TAG)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base G (14/15); new base A (6/11); total (20/26)
Fisher's exact test for biased strand distribution p-value = 5.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.81e-01

AATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGTGATGATCA  >  USA300TCH1516_ALE/2372881‑2373159

aaTCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAGCAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTa                                                                                                                                            >  1:419042/1‑141 (MQ=255)

  tCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATc                                                                                                                                          <  1:298751/141‑1 (MQ=255)

   cTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGATAAAATAACAATTAAGAACAGTATCg                                                                                                                                         >  1:63602/1‑141 (MQ=255)

   cTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCGGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCg                                                                                                                                         <  1:194827/141‑1 (MQ=255)

    tGAGAACAATGCTCTACAAGCTCTTGGTAATTTATTATCTTAAATAATACCTGCTTGAGTAGCAACAGCTACTCATATACAAGCTGTATCAAAGAAATCAAAAAATAAGAACGTTAAAATAACAATTAAGAACTGTAACGt                                                                                                                                        >  1:29876/1‑141 (MQ=255)

          aaaTGCTCTACCAGCTCTTGGTAATTTATTATATTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTtaataa                                                                                                                                  <  2:222528/140‑1 (MQ=255)

           aaTGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTaataat                                                                                                                                 <  2:202726/141‑1 (MQ=255)

             tGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTg                                                                                                                               <  1:194323/141‑1 (MQ=255)

              gCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGa                                                                                                                              >  2:228162/1‑141 (MQ=255)

                tctACGAGCTCTTTGTAATTTATTATCTTTCATAATACCTGCTTGATTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACt                                                                                                                            <  2:401650/141‑1 (MQ=255)

                    ccAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTggg                                                                                                                        >  1:152095/1‑141 (MQ=255)

                      aGCTCTTAGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTc                                                                                                                      <  2:368460/141‑1 (MQ=255)

                       gCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCt                                                                                                                     >  1:60578/1‑141 (MQ=255)

                              gTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACg                                                                                                              >  1:337102/1‑141 (MQ=255)

                                      ttatCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCaaaa                                                                                                      >  1:388243/1‑140 (MQ=255)

                                               ataataCCTGCTTGAGGAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCg                                                                                             <  1:288973/141‑1 (MQ=255)

                                               ataagaCCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCg                                                                                             <  1:88214/141‑1 (MQ=255)

                                                    aCCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCCACGAACGt                                                                                        >  2:168236/1‑141 (MQ=255)

                                                    aCCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGt                                                                                        >  1:328451/1‑141 (MQ=255)

                                                        gCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGt                                                                                    <  2:152095/141‑1 (MQ=255)

                                                        gCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGt                                                                                    <  1:261656/141‑1 (MQ=255)

                                                           tGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCa                                                                                 >  1:337677/1‑141 (MQ=255)

                                                           tGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCa                                                                                 <  1:250559/141‑1 (MQ=255)

                                                           tGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGATTCAAATGCAGCACCGAACGTTGGTTCa                                                                                 >  1:269134/1‑141 (MQ=255)

                                                              gTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGAACGGCACGTTGGTTCAATa                                                                              >  2:427/1‑141 (MQ=255)

                                                                     cAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACATGGATCTCTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGaa                                                                       >  2:194553/1‑141 (MQ=255)

                                                                                 tACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACaa                                                           >  1:179389/1‑141 (MQ=255)

                                                                                 tACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGAATAGGTAAACTAAATGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACaa                                                           >  1:314308/1‑141 (MQ=255)

                                                                                       cTGTATCAAAGAAATCAATAAATAAGAACTTTAAAATAAGAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTGTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAg                                                     <  2:153911/141‑1 (MQ=255)

                                                                                       cTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAg                                                     <  1:198462/141‑1 (MQ=255)

                                                                                           aTCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATgg                                                 <  1:288338/141‑1 (MQ=255)

                                                                                           aTCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATgg                                                 <  2:297234/141‑1 (MQ=255)

                                                                                                  aaaTCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGa                                          <  1:365923/141‑1 (MQ=255)

                                                                                                       aataaataAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGaatcaa                                     <  2:258125/141‑1 (MQ=255)

                                                                                                       aataaataAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGaatcaa                                     >  1:257354/1‑141 (MQ=255)

                                                                                                       aagagataaGAACGTTAAAATAACAATTAAGAACTATTGCGTTAATAATTGACTTGGGTGTTTAAACGCTTCAAATGCAGCACCGAACGGTGGTTCAATACTTGGAATCGTACCCACAATACCAGATGGCATTTGaatcaa                                     <  2:39653/136‑1 (MQ=255)

                                                                                                          aaataaGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATcc                                  >  2:383673/1‑141 (MQ=255)

                                                                                                            ataaGAACGTTAAAGTAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAg                                <  1:395269/141‑1 (MQ=255)

                                                                                                               aGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGa                             <  2:401546/141‑1 (MQ=255)

                                                                                                                gAACGTTAAAATAACAATTAAGAGCTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGaa                            <  1:72688/141‑1 (MQ=255)

                                                                                                                aaaCGTTAAACACACAATTAAGACCTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGaa                            <  1:281774/140‑1 (MQ=255)

                                                                                                                    ggtAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATa                        <  2:151005/139‑1 (MQ=255)

                                                                                                                               aaTTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGc             <  2:419042/141‑1 (MQ=255)

                                                                                                                                    aGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGtga        >  1:273753/1‑141 (MQ=255)

                                                                                                                                    aGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTAtga        >  1:252058/1‑141 (MQ=255)

                                                                                                                                       aCTATATCGTTAATAGTTGACTTGTGTCGTTAAACGCTTCAAATGCAGGACCGAACGTTGGTTCAATACTTTGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGtgatga     <  2:615/141‑1 (MQ=255)

                                                                                                                                          gTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGTGATGATCa  >  2:388335/1‑141 (MQ=255)

AATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGTGATGATCA  >  USA300TCH1516_ALE/2372881‑2373159

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