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
A29 F119 I1 R1	30	31.1	1326154	90.1%	1194864	128.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	754,446	A→G	L8P (CTC→CCC)	gltA ←	citrate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	754,446	0	A	G	96.4%	63.5 / NA	28	L8P (CTC→CCC)	gltA	citrate synthase
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (14/13); minor base C (0/1); total (14/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

AAGTGAAGCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCT  >  NC_000913/754324‑754570

aagtgaatCTTGGGTCAAAGGTGAACACTCCTTTTGAACGGATAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCATCAGCTGTATCCCCGTTGAGGGTGGGTTTTg                                                                                                                        <  2:239051/129‑1 (MQ=255)

    gaagCCTGGGTCAAAGGTGAACACACCTTTGGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCttt                                                                                                                    <  2:374868/129‑1 (MQ=255)

               cAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCACAGATGAGGGTGGGATTGCCGTTTGTATAACCCa                                                                                                         >  2:296528/1‑129 (MQ=255)

                  aGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCTTATCCTGTTTTTCAGTTGTATTTTTGTTGAGGGTGGGTTTTGCTTTTGGATCAGCCAttt                                                                                                      <  1:159698/129‑1 (MQ=255)

                      gAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGCGGGTTTTGGTTTTGAGTCAGCCATTTAAgg                                                                                                  >  2:267212/1‑129 (MQ=255)

                              cTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGCGCCATTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTAGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTa                                                                                          >  2:254083/1‑129 (MQ=255)

                                       cGAGAGTACGGATATCAATTACATCTTGACCCAGCATGCATATCAACACATACAATTAAACAGCTGTATCCACGTTGAGGGTGGGTTTTGCTTTTGTATCAGTCATTTAAGGTCTCCTTAGCGccctgt                                                                                 >  1:363684/1‑125 (MQ=255)

                                       cGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGTGGGTGGGTTTTGTTTTTGTATCAGTCATTTAAGGTCTCCTGAGCGCCTTAt                                                                                 <  1:517401/129‑1 (MQ=255)

                                             tACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCAAATCAAGTTCAACAGCTGTATACCCGTTGAGGGTGGGATTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTa                                                                           >  1:583081/1‑129 (MQ=255)

                                                 gATATCAATTACATCTTGTCCCAGCGTGCCTTTCAGCACATCCAGTTAAACGGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGAc                                                                       <  2:556257/129‑1 (MQ=255)

                                                    atCAATAACATCTTGACCCAGCGTGCCTTTCAGAACATCCAGTTCAACAGGTGTATGCCCGTTGAGGGTGGGGTTTGCTTTTGTCTCACCCATTCAAGGCCCGCTTAGCGCCTCATTGCGTAAGACTGc                                                                    >  2:649359/1‑129 (MQ=255)

                                                     tCAATAACATCTTGACCCCCCGTGCCTTTCAGAACATCCAATTAAACAACTATATACCCGCAGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGcc                                                                   >  1:304239/1‑129 (MQ=255)

                                                     tCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGcc                                                                   <  2:275870/129‑1 (MQ=255)

                                                               cTTGACCCTGAGTTTCTCTCAGCCCCTTTAGTTCTACAGCTGTCTCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCTGAACTTaaa                                                         <  2:272951/129‑1 (MQ=255)

                                                                ttGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGACGGTGGGATTTGCTTTTGTATCATCCCTTTAAGACTTCCTTACCGCGTTCTCGCGTACCACTGCCGGACCTCAAAt                                                        >  2:647873/1‑129 (MQ=255)

                                                                    cccAGCGTGCCTTTCAGCACATGCAGTTCAACAGGTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGc                                                    <  2:238943/129‑1 (MQ=255)

                                                                      cAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTTCGTAATCCTGCCGTAACTCAAATTTGCCt                                                  >  2:527446/1‑129 (MQ=255)

                                                                       aGCTTGCCTTTCAGCACATCCAGTGCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTACATTTGCCtt                                                 <  2:420740/129‑1 (MQ=255)

                                                                                ttCAGGACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCa                                        <  2:128362/129‑1 (MQ=255)

                                                                                        aTCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCt                                >  2:454341/1‑129 (MQ=255)

                                                                                          ccAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAATGTCTCCTTAGCGCCTTATTTCGTTATACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCttt                              <  1:267212/129‑1 (MQ=255)

                                                                                           cAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGTGTTATTTTGCTGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTa                             <  1:487760/129‑1 (MQ=255)

                                                                                            aGTTCAACAGCAGTATCCCCGTTGAGGGTGGGTTCTGCTTTTGTATCAGCCATTTCAGGTCTCCTTAGCGCCTTATTGGGTAATCATGTCGGAAATTAACTTTGCCTTCGAGAATAAACATGGCttcga                            >  2:52262/1‑126 (MQ=255)

                                                                                             gTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGATTTAGTATAAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTAGCTTTAcc                           >  1:310839/1‑129 (MQ=255)

                                                                                                                gTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGAATAAAAAAAACCATATAACGTAAGAATGCAGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTcgc        >  1:596983/1‑129 (MQ=255)

                                                                                                                   gAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTcgccgc     <  2:44553/129‑1 (MQ=255)

                                                                                                                     gggtgggtTTTGCTTTTGTATCAGCCATTTAAGGTATCCTTAGCGCCTTATTGCGTAAGACTGCCTTAACTTCCACTCGGCAACGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCACCGctc   >  2:639041/1‑129 (MQ=255)

                                                                                                                     gggTGCGTTTTGCTTTTGTATCAGCCATTTAAGGCCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGctc   <  2:458550/129‑1 (MQ=255)

                                                                                                                      ggTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTACATAGAGCCTTATTGCGTAAGACTGCCGGTACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACGCGTTTTTTATTTGGCTCGCCGctct  >  1:289119/1‑129 (MQ=255)

AAGTGAAGCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCT  >  NC_000913/754324‑754570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A