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	890,260	T→C	V39A (GTT→GCT)	gcvH →	Glycine cleavage system H protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	890,260	0	T	C	97.6%	158.3 / NA	42	V39A (GTT→GCT)	gcvH	Glycine cleavage system H protein
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (19/22); minor base A (1/0); total (20/22)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAATTAGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGTTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACGAAGAACTAGAAGATAGTC  >  USA300TCH1516_ALE/890126‑890403

taattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTa                                                                                                                                    >  4:283071/1‑148 (MQ=255)

taattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTa                                                                                                                                    <  3:29889/148‑1 (MQ=255)

taattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTa                                                                                                                                    <  3:28123/148‑1 (MQ=255)

taattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTa                                                                                                                                    <  3:28120/148‑1 (MQ=255)

 aattaGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTAc                                                                                                                                   <  3:158398/148‑1 (MQ=255)

     aggaggGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGa                                                                                                                               >  4:49075/1‑148 (MQ=255)

        aggGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAAc                                                                                                                            >  3:27082/1‑148 (MQ=255)

        aggGGATTCTCTTGGCAGTACCAAATGAATCGAAATATTCAAAAGAGCATGACTGGGTAAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAAc                                                                                                                            >  4:154644/1‑148 (MQ=255)

            gATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTACAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAgat                                                                                                                        <  3:235723/148‑1 (MQ=255)

               tctcTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAAc                                                                                                                            >  1:63035/1‑141 (MQ=255)

                    tGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAAt                                                                                                                <  3:252825/148‑1 (MQ=255)

                                          atatTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGt                                                                                          <  4:133506/148‑1 (MQ=255)

                                              tCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCg                                                                                      >  3:118605/1‑148 (MQ=255)

                                                      gCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGt                                                                                     <  1:57077/141‑1 (MQ=255)

                                                                   aaaGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTAt                                                                 >  3:336676/1‑148 (MQ=255)

                                                                                      cAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAt                                              <  3:336697/148‑1 (MQ=255)

                                                                                      cAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAt                                              <  3:362733/148‑1 (MQ=255)

                                                                                        ataatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAtct                                            <  4:367253/148‑1 (MQ=255)

                                                                                        ataatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAtct                                            <  4:2261/148‑1 (MQ=255)

                                                                                        ataatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAtct                                            <  3:325112/148‑1 (MQ=255)

                                                                                        ataatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAAtct                                            <  4:6080/148‑1 (MQ=255)

                                                                                          acttGGAACCACAGAATACGCACAAAGCGAGTTAGGGGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGCAGGAGATACTGTTGGTAGCGTAGAACCAGTTAAAACTGTATCAGAATTATATGCAcc                                                 <  1:61256/139‑1 (MQ=255)

                                                                                          aatTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATctct                                          <  3:24141/148‑1 (MQ=255)

                                                                                              ggAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTa                                      >  4:206359/1‑148 (MQ=255)

                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  4:337801/1‑148 (MQ=255)

                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  3:70798/1‑148 (MQ=255)

                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  3:69267/1‑148 (MQ=255)

                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  3:168270/1‑148 (MQ=255)

                                                                                                aaTCACAGAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  3:229584/1‑148 (MQ=255)

                                                                                                     caGAATACGCACAAAGCGAGTTAGGTGATATTGATTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTa                                      >  2:28370/1‑141 (MQ=255)

                                                                                                       gAATACGCACAAAGCGCGAAAGTTAACTTTGCTTTCGTTGAATTACCAGAATCAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTaaa                                    >  2:48921/1‑141 (MQ=255)

                                                                                                       gAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTg                             <  4:175229/148‑1 (MQ=255)

                                                                                                       gAATACGCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTg                             <  4:317312/148‑1 (MQ=255)

                                                                                                             gCACAAAGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCa                       <  4:108271/148‑1 (MQ=255)

                                                                                                                 aaaGCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACga                   >  3:43146/1‑148 (MQ=255)

                                                                                                                    gCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACgaaga                <  4:140416/148‑1 (MQ=255)

                                                                                                                    gCGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACgaaga                <  3:49075/148‑1 (MQ=255)

                                                                                                                     cGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACgaagaa               >  4:119333/1‑148 (MQ=255)

                                                                                                                     cGAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACgaagaa               >  4:119327/1‑148 (MQ=255)

                                                                                                                      gAGTTAGGTGATATTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACGAAGAAc              <  3:283071/148‑1 (MQ=255)

                                                                                                                                  atTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACGAAGAACTagaa         >  1:58947/1‑141 (MQ=255)

                                                                                                                                  atTGCTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTAACAGAAGAACTAGAAGATAGTc  >  3:3408/1‑148 (MQ=255)

TAATTAGGAGGGGATTCTCTTGGCAGTACCAAATGAATTGAAATATTCAAAAGAGCATGAATGGGTTAAAGTTGAAGGTAATGTAGCAATAATTGGAATCACAGAATACGCACAAAGCGAGTTAGGTGATATTGTTTTCGTTGAATTACCAGAAACAGATGATGAAATTAATGAAGGGGATACGTTTGGTAGCGTAGAATCAGTTAAAACTGTATCAGAATTATATGCACCAATCTCTGGTAAAGTAGTTGAAGTCAACGAAGAACTAGAAGATAGTC  >  USA300TCH1516_ALE/890126‑890403

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A