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
A5 F1 I2 R1	77	34.8	1608548	95.0%	1528120	114.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,237,322	G→A	I144I (ATC→ATT)	mglC ←	methyl‑galactoside transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,237,322	0	G	A	91.9%	101.7 / 1.7	37	I144I (ATC→ATT)	mglC	methyl‑galactoside transporter subunit
Reads supporting (aligned to +/- strand): ref base G (1/2); new base A (20/14); total (21/16)
Fisher's exact test for biased strand distribution p-value = 5.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01

ATGTAAGAGAGACGGAAACTCCCCAGCGCGACAAAGCCCTGAGCAAAGGTAGAGAAGCCACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACGATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAGCGCAATCGGCATCGTCGCCA  >  NC_000913/2237197‑2237455

aTGTAAGAGAGACGGAAACTCCCCAGCGCGACAAAGCCCTGAGCAAAGGTAGAGAAGCCACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGc                                                                                                                          >  1:153476/1‑139 (MQ=255)

      gagagaCGGAAACTCCCCAGCGCGACAAAGCCCTGAGCAAAGGTAGAGAAGCCACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCg                                                                                                                    <  2:630432/139‑1 (MQ=255)

           aCGGAAACTCCCCAGCGCGACAAAGCCCTGAGCAAAGGTAGAGAAGCCACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTa                                                                                                               >  2:277566/1‑139 (MQ=255)

            cGGAAACTCCCCAGCGCGACAAAGCCCTGAGCAAAGGTAGAGAAGCCACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTaa                                                                                                              >  2:395555/1‑139 (MQ=255)

                  cTCCCCAGCGCGACAAAGCCCTGAGCAAAGGTAGAGAAGCCACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACg                                                                                                        <  2:153476/139‑1 (MQ=255)

                                         aGCAAAGGTAGAGAAGCCACTGTCAGAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATa                                                                                 >  2:307695/1‑139 (MQ=255)

                                                   gagaAGCCACTGTCAAAACCAGAAATTGGCGACGCGCCGACAAAGGCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCg                                                                                                                    >  1:77238/1‑94 (MQ=255)

                                                   gagaAGCCACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCg                                                                                                                    <  2:77238/94‑1 (MQ=255)

                                                          cACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCaa                                                                >  2:635162/1‑139 (MQ=255)

                                                           aCTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCg                                                                                                     <  2:662353/101‑1 (MQ=255)

                                                           aCTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCg                                                                                                     >  1:662353/1‑101 (MQ=255)

                                                                         aaaTTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACGATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCAcc                                                 >  2:141012/1‑139 (MQ=255)

                                                                         aaaTTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCAcc                                                 >  2:455929/1‑139 (MQ=255)

                                                                         aaaTTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCAcc                                                 >  1:184836/1‑139 (MQ=255)

                                                                              ggCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATgg                                            <  1:277566/139‑1 (MQ=255)

                                                                                cGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCa                                                                             <  1:656748/104‑1 (MQ=255)

                                                                                cGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCa                                                                             >  2:656748/1‑104 (MQ=255)

                                                                                cGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGca                                          <  1:635162/139‑1 (MQ=255)

                                                                                  aCGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGcaca                                        <  1:120432/139‑1 (MQ=255)

                                                                                       ccGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACGATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACaa                                   <  1:141012/139‑1 (MQ=255)

                                                                                       ccGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACaa                                   <  1:455929/139‑1 (MQ=255)

                                                                                       ccGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACaa                                   <  2:184836/139‑1 (MQ=255)

                                                                                                      tAGAGCGAGTTGATGCCATAGACGATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAgcg                    <  2:79148/139‑1 (MQ=255)

                                                                                                          gCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGca                                          <  1:395159/113‑1 (MQ=255)

                                                                                                          gCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGca                                          >  2:395159/1‑113 (MQ=255)

                                                                                                          gCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAGCGCAAt                >  2:593436/1‑139 (MQ=255)

                                                                                                          gCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAGCGCAAt                >  1:239681/1‑139 (MQ=255)

                                                                                                          gCGAGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAGCGCAAt                >  2:420137/1‑139 (MQ=255)

                                                                                                             aGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGa                                      <  1:625622/114‑1 (MQ=255)

                                                                                                             aGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGa                                      >  2:625622/1‑114 (MQ=255)

                                                                                                             aGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAg                      <  1:209503/130‑1 (MQ=255)

                                                                                                             aGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAg                      >  2:209503/1‑130 (MQ=255)

                                                                                                             aGTTGATGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAGCGCAATCgg             >  1:694384/1‑139 (MQ=255)

                                                                                                                   tGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATgg                                            >  2:174685/1‑102 (MQ=255)

                                                                                                                   tGCCATAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATgg                                            <  1:174685/102‑1 (MQ=255)

                                                                                                                        tAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAGCGCAATCGGCATCGTCGCCa  >  1:97383/1‑139 (MQ=255)

                                                                                                                        tAGACAATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAGCGCAATCGGCATCGTCGCCa  >  2:683208/1‑139 (MQ=255)

ATGTAAGAGAGACGGAAACTCCCCAGCGCGACAAAGCCCTGAGCAAAGGTAGAGAAGCCACTGTCAAAACCAGAAATTGGCGACGCCCCGACAAAGTCGTAATAGAGCGAGTTGATGCCATAGACGATGATCATCGTGCCGAGCGTGGTAATGAACGGCGTCACGTTGAGATAAGCGATAATCAGACCGTTGATCAAACCGATCACCGCACCAATGGCACAGACAATCAGAATAACCAGCGCAATCGGCATCGTCGCCA  >  NC_000913/2237197‑2237455

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A