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
A0 F0 I1 R1	715	38.4	1606192	96.6%	1551581	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,767,445	(C)_7→8	intergenic (+90/‑265)	rnlB → / → yfjP	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,767,438	1	.	C	81.1%	102.9 / 17.0	37	intergenic (+83/‑272)	rnlB/yfjP	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein
Reads supporting (aligned to +/- strand): ref base . (6/1); new base C (11/19); total (17/20)
Fisher's exact test for biased strand distribution p-value = 3.35e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAA  >  NC_000913/2767301‑2767568

aGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c                                                                                                                                     >  2:30810/1‑139 (MQ=255)

  ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAGTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑ca                                                                                                                                  >  2:424865/1‑138 (MQ=255)

  ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c                                                                                                                                 <  2:695383/139‑1 (MQ=255)

  ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGACCAATATGATCAAATAGCATT‑AA‑cat                                                                                                                                   >  1:36484/1‑137 (MQ=255)

   ctctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑cc                                                                                                                                <  1:451351/139‑1 (MQ=255)

    tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑ccc                                                                                                                               <  1:722855/139‑1 (MQ=255)

            gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAGCTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTcaca                                                                                                                        >  1:566640/1‑139 (MQ=255)

                cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGt                                                                                                                    <  2:217938/139‑1 (MQ=255)

                cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c                                                                                                                                     >  2:277427/1‑123 (MQ=255)

                cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c                                                                                                                                     <  1:277427/123‑1 (MQ=255)

                 ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTc                                                                                                                   <  2:566640/139‑1 (MQ=255)

                 ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTc                                                                                                                   <  2:118757/139‑1 (MQ=255)

                  cGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑C‑CCCCCTCACAACGTCCt                                                                                                                 >  1:444778/1‑139 (MQ=255)

                         gTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGTATT‑AACC‑C‑CCCCCTcaca                                                                                                                        <  1:443764/126‑1 (MQ=255)

                         gTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTcaca                                                                                                                        >  2:443764/1‑126 (MQ=255)

                           aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CAA‑ACCTCTCACAACGTTCTTCAttagg                                                                                                         >  2:786295/1‑135 (MQ=255)

                              ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTcaca                                                                                                                        <  2:205768/121‑1 (MQ=255)

                              ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGt                                                                                                                    >  1:246505/1‑125 (MQ=255)

                              ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGt                                                                                                                    <  2:246505/125‑1 (MQ=255)

                              ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAac                                                                                                      <  2:690669/139‑1 (MQ=255)

                              ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCAAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTcaca                                                                                                                        >  1:205768/1‑121 (MQ=255)

                               cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAac                                                                                                      >  1:675218/1‑138 (MQ=255)

                               cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAac                                                                                                      <  2:675218/138‑1 (MQ=255)

                                  gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGt                                                                                                  >  2:643875/1‑139 (MQ=255)

                                   tCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGtt                                                                                                 <  1:295686/139‑1 (MQ=255)

                                    ccTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCa                                                                                                              >  1:282196/1‑125 (MQ=255)

                                    ccTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCa                                                                                                              <  2:282196/125‑1 (MQ=255)

                                                 ttttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc                                                                                   <  1:643875/139‑1 (MQ=255)

                                                                 tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACAACTAAATTTccc                                                                   <  1:424865/139‑1 (MQ=255)

                                                                         aaCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTa                                                           <  2:235331/139‑1 (MQ=255)

                                                                             aGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACtt                                                      <  2:444778/139‑1 (MQ=255)

                                                                              gTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACtt                                                      <  1:382365/139‑1 (MQ=255)

                                                                                         gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTc                                                                                                                   >  2:555970/1‑67 (MQ=255)

                                                                                         gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTc                                                                                                                   <  1:555970/67‑1 (MQ=255)

                                                                                         gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑C‑CCCCCTCCCAACGTCCTGGATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTc                                          >  2:117255/1‑139 (MQ=255)

                                                                                                                 gTCGAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACACCGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAAGCCTatg                   <  1:556224/139‑1 (MQ=255)

                                                                                                                 gTCCAATATGATCAAATAGCATTAAA‑C‑C‑CCCACTCACAACGTCCTGCATAGGGAACACGTATTCCCCTCTGCACCCACGACGAAATTTTCCCCCCTATAAACTTCTTAATAATGTCAACAATTATCTGGCAATCCTttg                   >  1:473268/1‑139 (MQ=255)

                                                                                                                 gTCCAATATGATCAAATAGCATT‑AA‑C‑CACCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCCCCCACGACTAAATTTCTCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatg                   >  1:51426/1‑139 (MQ=255)

                                                                                                                  tCCAATATGATCAAATAGCATTAAA‑C‑C‑CCCCCTCACAACGTCTTGCATAGGGAACACGTTTTCCCCTGTGCCCCCCCGACTAAATTTCCCCCCCTTTACACTTCTTAATAATGTTACCAATTTTCTGGAAATCCTatga                  >  2:210565/1‑139 (MQ=255)

                                                                                                                  tCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatga                  >  2:674555/1‑139 (MQ=255)

                                                                                                                  tCCAATATGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACATCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTACCCCACTTTAAAGTTTTCCATAATGTCACCAATTTTATGAAATTCCTacga                  >  1:428719/1‑139 (MQ=255)

                                                                                                                  tCCAATATGATCAAATAGCATT‑AA‑CTC‑CCCCCTCTCAACCTCCTGCATAGGGAACACGTTTTTCCCTGAGCACACACGAATCAAATTCCCCCCCCTTAAACTTCTCAACAGTATTCCTAATTTTCTTGAAATCCTatga                  >  2:11790/1‑139 (MQ=255)

                                                                                                                         tGATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCttt           <  2:36484/139‑1 (MQ=255)

                                                                                                                          gATCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTc          <  2:51426/139‑1 (MQ=255)

                                                                                                                            tCAAATAGCATT‑AACC‑C‑CCCCCTCACAACGTTCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCAACAATTTTCTGGAAATCCTATGATGCCTTTccc        >  1:442837/1‑139 (MQ=255)

                                                                                                                            tCAAATAGCATT‑AA‑C‑CACCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGACACCGATTTTCTGGAACTCCTATGATGCCTTTacc        >  2:715565/1‑139 (MQ=255)

                                                                                                                                  aGCATT‑AACC‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaaa  <  1:786295/139‑1 (MQ=255)

AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑C‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAA  >  NC_000913/2767301‑2767568

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A