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
A4 F28 I1 R1	128	54.7	1845674	99.3%	1832754	139.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,488,579	(C)_7→8	coding (1485/1503 nt)	yjgR ←	DUF853 domain‑containing protein YjgR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,488,572	1	.	C	97.8%	164.8 / ‑3.2	46	coding (1492/1503 nt)	yjgR	DUF853 domain‑containing protein YjgR
Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (27/18); total (27/19)
Fisher's exact test for biased strand distribution p-value = 4.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

TGTTAGCAAAGTGTGCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CT‑CCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCCGCGTGGTCCGGTAGTGCCGAACA  >  NC_000913/4488442‑4488697

tGTTAGCAAAGTGTGCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CT‑cccccccca                                                                                                                      >  1:650835/1‑138 (MQ=255)

   tAGCAAAGTGTGCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CT‑ccccccccagca                                                                                                                   <  2:372786/140‑6 (MQ=255)

    aGCAAAGTGTGCTTCGTTCATTCCTGAAAAATAATTAAAATTCGATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCaa                                                                                                                   >  2:93357/1‑140 (MQ=255)

    aGCAAAGTGTGCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCaa                                                                                                                   >  1:266581/1‑140 (MQ=255)

    aGCAAAGTGTGCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCaa                                                                                                                   >  2:300343/1‑140 (MQ=255)

           tgtgCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTcccc                                                                                                            >  1:678059/1‑140 (MQ=255)

              gCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAAc                                                                                                         <  2:266581/140‑1 (MQ=255)

              gCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAAc                                                                                                         >  1:464655/1‑140 (MQ=255)

                  cGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CT‑ccccccccagca                                                                                                                   <  1:736766/125‑6 (MQ=255)

                  cGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CT‑ccccccccagca                                                                                                                   >  2:736766/1‑120 (MQ=255)

                   gTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATccc                                                                                                    <  1:745231/140‑1 (MQ=255)

                      cATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCcgcg                                                                                                 <  2:347946/140‑1 (MQ=255)

                                               aaTATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTTATTCGTCACTTGGCGa                                                                        >  1:490671/1‑140 (MQ=255)

                                                      tGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGgcgc                                                                 >  1:449065/1‑140 (MQ=255)

                                                      tGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGgcgc                                                                 >  2:427108/1‑140 (MQ=255)

                                                      tGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGgcgc                                                                 >  2:518969/1‑140 (MQ=255)

                                                      tGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGgcgc                                                                 >  1:511427/1‑140 (MQ=255)

                                                      tGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGgcgc                                                                 >  2:715865/1‑140 (MQ=255)

                                                        cAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGAGTACAATCTGATTCGTCACTTGGCGAGCGGCGCtt                                                               >  2:635930/1‑140 (MQ=255)

                                                         aGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCttt                                                              >  1:630547/1‑140 (MQ=255)

                                                           tggggtgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGCTTCGTCACTTGGCGAGCGGCGCTTTTg                                                            >  2:398235/1‑140 (MQ=255)

                                                           tggggtgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTg                                                            >  1:656168/1‑140 (MQ=255)

                                                           tggggtgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTATT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTg                                                            >  1:815894/1‑140 (MQ=255)

                                                             gggtgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGc                                                          >  1:356693/1‑140 (MQ=255)

                                                             gggtgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGc                                                          >  1:346936/1‑140 (MQ=255)

                                                             gggtgggCATGATAAGACGCGCCAGCGTCGCATCAGACAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGc                                                          >  1:499939/1‑140 (MQ=255)

                                                              ggtgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGcc                                                         <  2:630547/140‑1 (MQ=255)

                                                               gtgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCa                                                        <  1:427108/140‑1 (MQ=255)

                                                               gtgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCa                                                        >  2:10435/1‑140 (MQ=255)

                                                                tgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGcc                                                         <  2:290495/138‑1 (MQ=255)

                                                                tgggCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGcc                                                         >  1:290495/1‑138 (MQ=255)

                                                                   gCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGt                                                    <  1:635930/140‑1 (MQ=255)

                                                                       gATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGGTTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGt                                                    >  1:488763/1‑136 (MQ=255)

                                                                       gATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGGTTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGt                                                    <  2:488763/136‑1 (MQ=255)

                                                                       gATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGc                                                <  1:518969/140‑1 (MQ=255)

                                                                        aTAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGca                                               >  1:209781/1‑140 (MQ=255)

                                                                           aGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGcacca                                            <  2:656168/140‑1 (MQ=255)

                                                                                 gcCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCAt                                      >  1:230468/1‑140 (MQ=255)

                                                                                  ccAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCACTTTTGGCCATTGTTTGCACCACACCAtc                                     >  2:267458/1‑140 (MQ=255)

                                                                                      cGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGtt                                                   >  2:865285/1‑122 (MQ=255)

                                                                                      cGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGtt                                                   <  1:865285/122‑1 (MQ=255)

                                                                                                 gCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTTATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCcgcg                      <  2:490671/140‑1 (MQ=255)

                                                                                                 gCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCcgcg                      <  1:535699/140‑1 (MQ=255)

                                                                                                 gCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCACTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCcgcg                      <  1:267458/140‑1 (MQ=255)

                                                                                                    aaGACAAATCTCGCCTGACTTCCCTTCTTCCC‑CCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACCCCATCTTTCTTCCCGCCGCGTgg                   <  1:321905/140‑1 (MQ=255)

                                                                                                                gCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCCGCGTGGTCCGGTAGTGcc       <  2:449065/140‑1 (MQ=255)

                                                                                                                gCCTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCCGCGTGGTCCGGTAGTGcc       >  2:345489/1‑140 (MQ=255)

                                                                                                                  cTGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCCGCGTGGTCCGGTAGTGCCGa     <  1:634003/140‑1 (MQ=255)

                                                                                                                   tGACTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCACTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCCGCGTGGTCCGGTAGTGCCGaa    <  1:393665/140‑1 (MQ=255)

                                                                                                                     aCTTACCTTCTT‑CTCCCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCCGCGTGGTCCGGTAGTGCCGAACa  <  1:715865/140‑1 (MQ=255)

TGTTAGCAAAGTGTGCTTCGTTCATTCCTGAAAAATAATTAAAATTCAATATATTGCAGTGGGGTGGGCATGATAAGACGCGCCAGCGTCGCATCAGGCAAAGACAAATCTCGCCTGACTTACCTTCTT‑CT‑CCCCCCCAGCAAACTCCCCAACATCCCGCGTACAATCTGATTCGTCACTTGGCGAGCGGCGCTTTTGGCCATTGTTTGCACCACACCATCTTTCTTCCCGCCGCGTGGTCCGGTAGTGCCGAACA  >  NC_000913/4488442‑4488697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A