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
A7 F1 I2 R1	766	64.2	3232166	90.9%	2938038	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,531,605	T→C	T279A (ACA→GCA)	yhgE ←	DUF4153 family putative inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,531,605	0	T	C	90.9%	93.0 / 0.2	33	T279A (ACA→GCA)	yhgE	DUF4153 family putative inner membrane protein
Reads supporting (aligned to +/- strand): ref base T (1/2); new base C (13/17); total (14/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.43e-01

ACCGCCAGCACGCCCTGCAAGCGGTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGTCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATCGCGCTCAGGCCCGTAAACGGCAGGGTG  >  NC_000913/3531469‑3531738

aCCGCCAGCACGCCCTGCAAGCGGTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGccc                                                                                                                                     >  2:226039/1‑139 (MQ=255)

    ccAGCACGCCCTGCAAGCGGTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAggg                                                                                                                                 >  2:1485325/1‑139 (MQ=255)

               tGCAAGCGGTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAggg                                                                                                                                 <  2:867337/128‑1 (MQ=255)

               tGCAAGCGGTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAggg                                                                                                                                 >  1:867337/1‑128 (MQ=255)

               tGCAAGCGGTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCtt                                                                                                                      >  2:1232416/1‑139 (MQ=255)

                    gCGGTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGc                                                                                                                 <  2:1435892/139‑1 (MQ=255)

                       gTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGTCCAGGGAAGTGACGCTTTTTGCGGa                                                                                                              >  2:1396782/1‑139 (MQ=255)

                           aCAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATcgc                                                                                                          <  2:295609/139‑1 (MQ=255)

                                  aGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAAt                                                                                                   <  1:226039/139‑1 (MQ=255)

                                    ccGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGTCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAg                                                                                                 <  1:119131/139‑1 (MQ=255)

                                    ccGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGTCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAg                                                                                                 <  1:1396782/139‑1 (MQ=255)

                                                 cccGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGAt                                                                                       >  2:1615669/1‑136 (MQ=255)

                                                 cccGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGAt                                                                                       <  1:1615669/136‑1 (MQ=255)

                                                      aGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACaa                                                                                                    >  2:879519/1‑118 (MQ=255)

                                                      aGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACaa                                                                                                    <  1:879519/118‑1 (MQ=255)

                                                                     gcggcgACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCa                                                                >  1:75736/1‑139 (MQ=255)

                                                                                       aGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATcgcg                                                                                                         >  1:415122/1‑80 (MQ=255)

                                                                                       aGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATcgcg                                                                                                         <  2:415122/80‑1 (MQ=255)

                                                                                            aGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGAtg                                         <  1:304644/139‑1 (MQ=255)

                                                                                                      aaaGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGaaa                               <  1:1232416/139‑1 (MQ=255)

                                                                                                        aGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATa                                                                                                  <  1:1610363/70‑1 (MQ=255)

                                                                                                        aGCGGTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATa                                                                                                  >  2:1610363/1‑70 (MQ=255)

                                                                                                           ggTTTTAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATcgcg                          >  2:1153251/1‑139 (MQ=255)

                                                                                                              tttAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATCGCGCTc                       <  2:608358/139‑1 (MQ=255)

                                                                                                               ttAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATa                                                                                                  >  1:166209/1‑63 (MQ=255)

                                                                                                               ttAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATa                                                                                                  <  2:166209/63‑1 (MQ=255)

                                                                                                               ttAATCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATCGCGCTCa                      <  2:536459/139‑1 (MQ=255)

                                                                                                                  aTCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCTATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATCGCGCTCAGGc                   <  1:1153251/139‑1 (MQ=255)

                                                                                                                  aTCAGGCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATCGCGCTCAGGc                   >  2:81033/1‑139 (MQ=255)

                                                                                                                      ggCAACGCAACGGCCCTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATCGCGCTCAGGCCCGt               >  2:1219708/1‑139 (MQ=255)

                                                                                                                       gcaacgcaacGGCCCTGCCCAGGGAAGTGACGCTTTTTGCg                                                                                                                >  1:1440327/1‑41 (MQ=255)

                                                                                                                       gcaacgcaacGGCCCTGCCCAGGGAAGTGACGCTTTTTGCg                                                                                                                <  2:1440327/41‑1 (MQ=255)

                                                                                                                                   cccTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATCGCGCTCAGGCCCGTAAACGGCAGGGtg  <  1:1219708/139‑1 (MQ=255)

                                                                                                                                     cTGCCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAAt                                                                                                   <  1:1338267/40‑1 (MQ=255)

ACCGCCAGCACGCCCTGCAAGCGGTCGACAGTCCAGCCGTACTGAGCGACCCGCAGCCATAACGCCCAGGCGGCGACGAACACATACAGCGGAGCAACCAGCAAAGCGGTTTTAATCAGGCAACGCAACGGCCCTGTCCAGGGAAGTGACGCTTTTTGCGGATCGCGGACAATAGCCATTAAGATCAATTGCAAAAAGGCCAGCGTCAACAGCAACCCGGCGGCGGAGATGTGGCGAGAAATCGCGCTCAGGCCCGTAAACGGCAGGGTG  >  NC_000913/3531469‑3531738

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