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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,534,187	A→G	E41G (GAA→GGA)	ptsI →	PEP‑protein phosphotransferase of PTS system (enzyme I)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,534,187	0	A	G	97.1%	119.8 / ‑3.6	34	E41G (GAA→GGA)	ptsI	PEP‑protein phosphotransferase of PTS system (enzyme I)
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (18/15); total (18/16)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.05e-01

AAAATCAGTCACAAGTAAGGTAGGGTTATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGAACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCATATTATGCTGCTCGAAGATGAGGAGCTGGAGC  >  NC_000913/2534039‑2534324

aaaaTCAGTCACAAGTAAGGTAGGGTTATGATTTCAGGCATTTTAACATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGAc                                                                                                                                         <  1:225944/151‑1 (MQ=255)

    tCAGTCACAAGTAAGGTAGGGTTATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGttt                                                                                                                                     >  1:622697/1‑151 (MQ=255)

       gTCACAAGTAAGGTAGGGTTATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCt                                                                                                                                  <  1:377512/151‑1 (MQ=255)

        tCACAAGTAAGGTAGGGTTATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTg                                                                                                                                 >  2:45850/1‑151 (MQ=255)

                    tAGGGTTATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTAATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGcc                                                                                                                     >  2:631881/1‑151 (MQ=255)

                     aGGGTTATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGcc                                                                                                                     >  2:363062/1‑150 (MQ=255)

                            tGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATc                                                                                                             >  2:507222/1‑151 (MQ=255)

                                  cAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGccc                                                                                                        <  2:413038/150‑1 (MQ=255)

                                  cAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCa                                                                                                       <  2:55448/151‑1 (MQ=255)

                                    ggCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGc                                                                                                     <  2:97049/151‑1 (MQ=255)

                                     gCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCt                                                                                                    >  1:344512/1‑151 (MQ=255)

                                          ttAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGaa                                                                                                >  2:151329/1‑150 (MQ=255)

                                                 ccccGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCa                                                                                         <  1:387082/150‑1 (MQ=255)

                                                 ccccGGGTATCGCTTTCGGTAAAGATCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGAACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCaa                                                                                        <  1:99139/151‑1 (MQ=255)

                                                  cccGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGt                                                                                                                        <  1:542872/118‑1 (MQ=255)

                                                  cccGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGt                                                                                                                        >  2:542861/1‑118 (MQ=255)

                                                    cGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAAc                                                                                     <  1:151334/151‑1 (MQ=255)

                                                                  ggTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGaaa                                                                       <  2:579831/151‑1 (MQ=255)

                                                                             gCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCTGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTga                                                             >  1:600964/1‑150 (MQ=255)

                                                                              cTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTga                                                             >  1:307302/1‑149 (MQ=255)

                                                                                  tGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGaaa                                                        >  1:293494/1‑150 (MQ=255)

                                                                                    aaaGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAaag                                                     <  1:149954/151‑1 (MQ=255)

                                                                                     aagaagACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGaaaa                                                       >  2:85146/1‑148 (MQ=255)

                                                                                           aCGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCAt                                              >  1:357828/1‑151 (MQ=255)

                                                                                             gAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCt                                            <  2:343244/151‑1 (MQ=255)

                                                                                                  tGTCGTTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGa                                        >  1:386759/1‑150 (MQ=255)

                                                                                                    tCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAgg                                     >  1:482747/1‑151 (MQ=255)

                                                                                                     cATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAgg                                     <  1:187554/150‑1 (MQ=255)

                                                                                                           ccGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCAtatt                              <  1:257969/151‑1 (MQ=255)

                                                                                                            cGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGGGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACG‑AAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCAtattat                            <  2:66020/151‑1 (MQ=255)

                                                                                                                        tCTGCCGACCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCATATTATGCTGCTCGaa                  <  2:186210/150‑1 (MQ=255)

                                                                                                                               aCCAGGTTGATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCATATTATGCTGCTCGAAGATgagg           >  2:402602/1‑150 (MQ=255)

                                                                                                                                  aGGTTAATCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCATATTATGCTGCTCGAAGATGAGGAGCt       >  2:43068/1‑151 (MQ=255)

                                                                                                                                         tCAGGAAGTTGGACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCATATTATGCTGCTCGAAGATGAGGAGCTGGAGc  >  2:397418/1‑149 (MQ=255)

AAAATCAGTCACAAGTAAGGTAGGGTTATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGAACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCATATTATGCTGCTCGAAGATGAGGAGCTGGAGC  >  NC_000913/2534039‑2534324

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A