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
A14 F1 I1 R1	71	51.6	2219666	95.9%	2128659	118.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,240,094	T→C	A85A (GCA→GCG)	mglB ←	methyl‑galactoside transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,240,094	0	T	C	97.5%	148.0 / NA	40	A85A (GCA→GCG)	mglB	methyl‑galactoside transporter subunit
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (20/19); minor base A (1/0); total (21/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGCTTTGTCGTAGCTATCCAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGTGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATCTTGCTCAATAGCCTTGCGCACTACA  >  NC_000913/2239964‑2240226

agGCTTTGTCGTAGCTATCCAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCAc                                                                                                                              >  1:93479/1‑139 (MQ=255)

    tttGTCGTAGCTATCCAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCt                                                                                                                          >  2:157189/1‑139 (MQ=255)

    tttGTCGTAGCTATCCAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCt                                                                                                                          >  2:906726/1‑139 (MQ=255)

      tGTCGTAGCTATCCAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCttt                                                                                                                        >  2:436677/1‑139 (MQ=255)

              cTATCCAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTCTCGCCAGCa                                                                                                                <  2:744763/139‑1 (MQ=255)

                  ccAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATAc                                                                                                            >  1:215599/1‑139 (MQ=255)

                   cAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACg                                                                                                           <  1:139403/139‑1 (MQ=255)

                   cAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACg                                                                                                           <  2:907294/139‑1 (MQ=255)

                       gcCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGa                                                                                                       >  1:610950/1‑139 (MQ=255)

                        ccTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGAt                                                                                                      >  2:360669/1‑139 (MQ=255)

                                gaCGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGt                                                                                              <  1:698028/139‑1 (MQ=255)

                                   ggTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCa                                                                                                                >  2:649230/1‑118 (MQ=255)

                                   ggTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCa                                                                                                                <  1:649230/118‑1 (MQ=255)

                                     ttCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGc                                                                                         >  2:641567/1‑139 (MQ=255)

                                       cTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGa                                                                                                       >  1:594887/1‑123 (MQ=255)

                                       cTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGa                                                                                                       <  2:594887/123‑1 (MQ=255)

                                          tgttgAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGa                                                                                    >  1:330834/1‑139 (MQ=255)

                                                     accaccGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCt                                                                         <  1:360669/139‑1 (MQ=255)

                                                        accGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTgag                                                                      <  1:157189/139‑1 (MQ=255)

                                                           ggCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAAt                                                                   <  2:946583/139‑1 (MQ=255)

                                                                 ttttGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAAtcattca                                                             >  1:600660/1‑139 (MQ=255)

                                                                   ttGCCCACACGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATtcatc                                                           >  1:816018/1‑139 (MQ=255)

                                                                         aggcgaTTTCTCAATCCCGGTACCCGCAGCTGCCGCGTCAACCAGGCTGATTGCCTGCGCCTTCGCCCCTTTCCCCAGCAATACGTCTATCTGTTCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCagcagc                                                     <  1:60399/137‑1 (MQ=255)

                                                                                      aTCACCGTACCCGCAGCTGCCGGGTCAACCAGTTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGgcg                                        <  2:1044865/139‑1 (MQ=255)

                                                                                       tCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGgcgc                                       <  1:135893/139‑1 (MQ=255)

                                                                                           cGTCCCCGGAGCGGCCGGGTCAAGCAGGTTCATCGCCAGAGTCTCCACCCCTTTCCCCAGCCATACGTCGGTCTGATAGTTCTGCTTGGACTTGTCATCCTGAGAATCATTCATCAGCAGCAGAACATCTGGCGCggta                                   >  1:871972/1‑137 (MQ=255)

                                                                                           cGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGAc                                                                                   <  2:312515/91‑1 (MQ=255)

                                                                                           cGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGAc                                                                                   >  1:312515/1‑91 (MQ=255)

                                                                                           cGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCt                                   >  2:186574/1‑139 (MQ=255)

                                                                                           cGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCt                                   >  2:514433/1‑139 (MQ=255)

                                                                                                   cAGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATc                           >  1:312478/1‑139 (MQ=255)

                                                                                                   aaGCTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATc                           <  2:842856/138‑1 (MQ=255)

                                                                                                      cTGCCGGGTCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATCTTg                        <  1:436677/139‑1 (MQ=255)

                                                                                                              tCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAg                                                                                                                  >  2:200097/1‑41 (MQ=255)

                                                                                                              tCAACCAGGTTGATTGCCAGCGCCTTCACCCCTTTCGCCAg                                                                                                                  <  1:200097/41‑1 (MQ=255)

                                                                                                                     ggTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATCTTGCTCAATAGCCTTgcg         <  1:514433/139‑1 (MQ=255)

                                                                                                                     ggTTGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATCTTGCTCAATAGCCTTgcg         <  1:201943/139‑1 (MQ=255)

                                                                                                                       ttGATTGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATCTTGCTCAATAGCCTTGCGCa       >  1:1017858/1‑139 (MQ=255)

                                                                                                                           ttGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATCTTGCTCAATAGCCTTGCGCACTAc   <  1:641567/139‑1 (MQ=255)

                                                                                                                            tGCCAGCGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATCTTGCTCAATAGCCTTGCGCACTACa  >  2:312990/1‑139 (MQ=255)

AGGCTTTGTCGTAGCTATCCAGCGCCTTACGAGACGGTTCTTTGTTGAAGAAAACCACCGGCACGTTTTGCCCACGCGCTTTCTCAATCACCGTACCCGCAGCTGCCGGGTCAACCAGGTTGATTGCCAGTGCCTTCACCCCTTTCGCCAGCAATACGTCGATCTGATCGTTCTGCTTGGACTGGTCATTCTGAGAATCATTCATCAGCAGCTGAACATCTGGCGCGGCTTTCGCATCTTGCTCAATAGCCTTGCGCACTACA  >  NC_000913/2239964‑2240226

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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